The Pamirs are a combination of east-west and north-south ranges, with the former predominating. The east-west Trans-Alay Range (Trans-Alai Range), which forms the northern frame of the Pamirs, falls steeply to the intermontane Alay Valley. The high central part of the range, between the Tersagar Pass on the west and Kyzylart on the east, averages between 19,000 and 20,000 feet (5,800 and 6,100 metres), reaching its highest point at Lenin Peak, 23,405 feet. South from the Trans-Alay extend three north-south ranges. Of these the western, the Akademiya Nauk Range, and the central, Zulumart, are relatively short; and the eastern, the Sarykol Range, forms the eastern border of the Pamirs. The area east of the Sarykol Range is sometimes called the Chinese Pamirs.

The north-south Akademiya Nauk Range enters into the northwestern Pamir system, where it rises into a huge barrier, reaching 24,590 feet (7,495 metres) in Communism Peak, the highest point in the Pamirs. The eastern slope of the Akademiya Nauk Range is covered on the south face by the Fedchenko Glacier. The western slope intersects other ranges that lie still farther to the west: the Peter I Range, with Moscow Peak (22,260 feet); the Darvaz Range, with Arnavad Peak (19,957 feet); and the Vanch and Yazgulem ranges, with Revolution Peak (22,880 feet). The ranges are separated by deep ravines. To the east of the Yazgulem Range, in the central portion of the Pamirs, is the east-west Muzkol Range, reaching 20,449 feet in Soviet Officers Peak. South of it stretches one of the largest ranges of the Pamirs, called Rushan on the west and Bazar-dara or Northern Alichur on the east. Still farther south are the Southern Alichur Range and, to the west of the latter, the Shugnan Range. The extreme southwestern Pamirs are occupied by the Shakhdarin Range, composed of north-south (Ishkashim Range) and east-west elements, rising to Mayakovsky Peak (19,996 feet) and Karl Marx Peak (22,067 feet). In the extreme southeast, to the south of Lake Zorkul (Sarī Qūl), lies the east-west Vākhān Mountains.

It is customary to divide the Pamirs into a western area and an eastern area, distinguished by their forms of relief. In the eastern Pamirs a medium-mountain relief predominates on a high raised foundation. While the heights above sea level average 20,000 feet or more, the relative heights of the peaks above their foundation do not in most cases exceed 3,300 to 5,900 feet. The ranges and massifs have mainly rounded contours, and the wide and flat-bottomed valleys and troughs between them, situated at heights of 12,100 to 13,800 feet, are occupied either by quietly running, meandering rivers or by dry channels. The valleys and slopes of the ranges are covered by layers of loose material.

In the western Pamirs the relief is high-mountain and sharply disjointed, alternating between low ranges and alpine ridges capped by snows and glaciers; and there are deep, narrow ravines with high, rapid rivers. The valleys and depressions are filled with debris, so that almost the only suitable places for human settlement are the alluvial fans in the valleys of tributaries of the Panj River. The transition from the eastern-Pamirs type of relief to the western-Pamirs type occurs gradually. The conventional boundary is a line joining the ridge of the Zulumart Range with Karabulak Pass in the Muzkol Range; from Pshart Pass it follows the ridge of the Northern Alichur Range to Lakes Yashilkul and Sarez, where it turns south to the valley of the Pamir River.

Like the adjacent Hindu Kush and Karakoram mountains to the south, the Pamirs exhibit considerable glaciation as a result of high winter snowfall. The Fedchenko Glacier dominates the central Pamir massif, with other glaciers, similarly named for 19th-century Russian scientists (e.g., Garmo and Grumm-Grzhimaylo), feeding into it. Glaciation is less extensive in the Alay and Trans-Alay mountains.

Some meltwater from the Pamirs flows to the Tarim Basin in China, but the vast bulk drains into the Panj River and its tributaries. There are large irrigation projects associated with the Kyzylsu-Surkhob-Vakhsh river system (each of the rivers flows successively into the next). The Amu Darya (ancient Oxus River), formed by the confluence of the Vakhsh and the Panj, conveys meltwater to other irrigation projects downstream. Seismic activity periodically interrupts the flow of rivers; Lake Sarez in the Murgab River valley was formed by massive landslides that dammed the river.

The Pamirs are divided into three broad zones according to the characteristics of their rock formations: the northern, central, and southern Pamirs. The southern zone consists of metamorphic rocks (gneiss, quartzite, marble, and others) to which a majority of researchers attribute a Precambrian age (more than 540 million years ago). The zone on the whole represents a huge anticline, or series of stratified arches. The central zone of the Pamirs contains limestone, sandstone, and shale rocks of the Jurassic, Triassic, and Permian periods (286 to 144 million years ago) and also red-coloured rocks of the Early Cretaceous Period (144 to 97.5 million years ago). There are some marine rocks from the first half of the Paleozoic Era (i.e., about 540 to 400 million years ago) and lava and tuffaceous rocks of the Paleocene Epoch (66.4 to 57.8 million years ago). The structure of the central Pamirs is that of a huge syncline (an inverted arch caused by fracturing); it is separated from the northern Pamirs by a deep fracture.

In the structure of the northern Pamirs, two subzones can be discerned: a Paleozoic zone and a zone beyond the Alay Mountains, which is composed of more recent deposits. The Paleozoic subzone of the northern Pamirs is a huge anticline with a complex internal structure. It is separated from the Trans-Alay subzone by the Karakul fracture, through which flows the Kyzylsu-Surkhob-Vakhsh river system. The Trans-Alay subzone is highly complex. Its western part is a fan-shaped anticline in the centre of which emerge Jurassic deposits; radiating outward are more recent, dislocated rocks of the Early Cretaceous. The eastern part has Cretaceous and Paleocene deposits in a system of conflicting folds. Because of the numerous overthrusts, or horizontal faults, in some places the layers overlap each other. On the north the Trans-Alay subzone is bounded by the deep Trans-Alay fracture, separating the Pamirs from the Alay system. Seismic records register some 2,500 earthquakes each year, with a major event occurring approximately every 15 years. Mudflows from severe storms also constitute a natural hazard.

The climate of the Pamirs is arid and continental, typified by frigid winters and warm, relatively dry summers. In the western valleys convectional storms, in combination with cyclonic storms, are common in the summer. Many weather patterns of the region are associated with the so-called Afghan winds that form in northwestern Afghanistan, intensify over the horseshoe ridges of the lower Pamirs, and bring summer dust storms and subsequent rain to the western mountains. Snowfall is substantial in the western valleys; the village of Sangvor, for example, at an elevation of 7,000 feet, has a snow cover of up to four feet from November to April. The growing season lasts 200 days in Sangvor but reaches 230 days in the deep valley of the Panj at Khorugh and Qalaikhum. At the highest elevations, snowfall equals that of the Karakorams to the southeast; glaciation is considerable. Temperatures range from summer daily highs of 73° F (23° C) and winter lows of 1° F (−17° C) at Murghob in the high eastern Pamirs to 81° F (27° C) in summer and 21° F (− 6° C) in winter at Garm in the lower western Pamirs; isolated outposts in the eastern Pamirs record temperatures below −58° F (−50° C) in winter.

In their vegetation, the eastern Pamirs bear a striking resemblance to the treeless western portion of the Plateau of Tibet. Large expanses of bog, interspersed with artemisia and ephedra on higher ground, typify the flora of these regions. The western Pamirs present a striking contrast. The forced emigration of mountain residents, which started in the late 1930s, has halted the overgrazing and cutting of firewood that has continued in adjoining ranges such as the Hindu Kush and the Karakorams. Since the exodus, juniper has regenerated on the valley slopes, caespitose shrubs have become established on the drier margins, and erosion has halted. Watercourses above 6,500 feet are lined with willow, thornbushes, oleander, poplar, and occasional birch. High-altitude pastures, above 10,000 feet, are rarely grazed by cattle.

The high tablelands of the eastern Pamirs are the prime breeding area of the mountain goat and the argali (Marco Polo) wild sheep; occasional sightings of blue sheep and urial are reported. Ibex are common where human activity is minimal, and markhor inhabit the lower ranges between the Panj and Vakhsh rivers. Brown bear feed on the abundant marmots, as do wolves. Relatively strict prohibitions against the hunting of wild sheep and goats have resulted in sufficient prey to support a small population of snow leopards. The lammergeier (bearded vulture) and the Himalayan griffon frequent the highest peaks, while partridge, pheasant, and snow cock are found in the western mountains. Large numbers of migratory waterfowl flying between Siberia and South Asia visit the eastern Pamirs.

Turkic-speaking Kyrgyz populate the eastern Pamirs, while Mountain Tajik and other Tajik groups live in the western valleys. The Mountain Tajik are Ismāʿīlī Shīʿite Muslims who formerly spoke Wakhi, a language related to those spoken in the Vākhān and Badakhshān regions of Afghanistan, in northernmost Chitrāl and Gilgit districts of Pakistan, and in the Sarykol region of western China. They presently speak several eastern Iranian languages, and almost all, in addition, speak the Persian dialect common to the lowland-dwelling people of Tajikistan and Afghanistan, who are largely Sunnite Muslims.

In the portion of the Pamirs in the Gorno-Badakhshan autonomous region of Tajikistan, nine-tenths of the population lives above 5,000 feet, and no settlement is located below 11,500 feet in the Kyrgyz sector. Of those residing in the eastern area, three-fifths migrate in the course of their annual pastoral tasks. At high altitude, the Kyrgyz exhibit much greater longevity and lower infant mortality than the Tajik. Substantial population movement has occurred since 1940, when the majority of the residents of the western Pamirs were forcibly removed to the irrigated cotton communes established on the broad river plains in Tajikistan. Agropastoral activities, often associated with communal farms, occupy the remaining inhabitants of the Pamirs. Population pressure in Tajikistan—which has a high birth rate and a large proportion of its population living in poverty—has made it necessary to establish new settlements and farms in the western Pamir valleys. This resettlement of formerly depopulated valleys is most evident in the Surkhob and Obikhingou valleys upstream from the huge hydroelectric dams at Norak and Rogun (Ragoon) on the Vakhsh River.

The high-elevation pastoralism practiced in the eastern Pamirs is devoted to yaks and related crossbreeds, sheep, and goats; barley and potatoes, pulses, rapeseed, and root vegetables constitute the main crops of this region. In the valleys of the western Pamirs, the government has mandated the cultivation of cotton and other crops. Large orchards—notably of apple, pear, and apricot, as well as vineyards—line many western valleys and foothills between 5,000 and 6,500 feet. Wheat is the dominant grain and corn (maize) the chief winter fodder. Cattle are replacing sheep and goats as principal livestock in the western valleys.

Motor-vehicle tracks reach all settlements in the Pamirs, and there is frequent air service to many small towns. Large passenger helicopters serve isolated locations on an infrequent basis. A major frontier road facilitates the movement of military garrisons in the Tajik and Kyrgyz portions of the Pamirs, and jeep tracks constructed in the 1980s support the Mountain Tajik living in the Vākhān region of Afghanistan. A major route through the old Karatikin Silk Road up the Surkhob and Kyzylsu rivers and the Alay Valley links Tajikistan with the major city of Osh in Kyrgyzstan. In the Chinese Pamirs the extension of the Karakoram Highway serves the Sarykol and Subashi pamir through the western extension of the Kunlun Mountains.

From the 1st through the 7th century AD, three branches of the Silk Road crossed the Pamirs. The 2nd-century Alexandrian scholar Ptolemy referred to the mountains as Comedae in his Guide to Geography. Troops of T'ang-dynasty China invaded the Pamirs in 747 but withdrew shortly thereafter. Marco Polo may have traversed the Vākhān region en route to Cathay, but it was not until 1603 when the Spanish Jesuit missionary Benedict de Goes traveled through the area and news of his findings was reported that it became known to Europe. As Konstantin Petrovich Kaufmann (Kaufmann, Konstantin Petrovich) conquered successive Central Asian khanates for Russia during the mid-19th century, British representatives—such as John Wood in the 1830s—sought a suitable physiographic boundary between Russian and British India. The legendary journeys of the Englishman Ney Elias brought an enlightened European view of the region and its peoples, one without military or political bias. Political control of the mountains was settled in 1891 when tsarist forces rebuffed the British at Bozai Gombaz (Bazai Gombad) in the southern Pamirs. Russian and British negotiators subsequently established the new buffer state of Afghanistan—including the narrow Wakhan Corridor (now the Vākhān region)—between their respective territories. The boundaries between China and Tajikistan and Kyrgyzstan in the Pamirs, however, have remained in dispute.

Exploration in the late 19th century was dominated by Russian scientists, who studied glaciation, geology, botany, and zoology. During this period, expeditions by other countries became infrequent, the Danish expedition of 1898–99 signaling the end of indiscriminate European incursion into Russian-controlled Central Asian territory. Other expeditions, including the much-touted foray by the British statesman Lord Curzon in 1894, only scouted the fringes of the Pamirs.

During the Soviet period, explorations in the Pamirs became systematic. In 1928 an expedition explored the region of the Fedchenko Glacier, making possible the first accurate topographical maps of the northwestern Pamirs. This was followed in the early 1930s by the establishment of a high-altitude hydrologic and meteorologic observatory—the first of its kind—at an altitude of about 15,700 feet on a lateral moraine of the glacier. The laboratory has produced much valuable scientific data on the physical properties of the Pamirs. In one study, the superior adaption to high-altitude living by the Asiatic Kyrgyz, compared to the European Tajik, has been a subject of physiological research. Many mountain-climbing and trekking groups visit the Pamir region each year; most activity occurs in the Trans-Alay Range, including Lenin Peak.