Torrey was educated at the College of Physicians and Surgeons in New York City (M.D., 1818), where he became a cofounder of the Lyceum of Natural History, later the New York Academy of Sciences. In 1817 he and several members of the Lyceum prepared A Catalogue of Plants Growing Spontaneously within Thirty Miles of the City of New York, which came to be known as “Torrey's catalog.” He made an extensive study of the plants of the northeastern U.S., and the unidentified plants collected on government expeditions to the western states were sent to him for study. After publication of his Flora of the Northern and Middle Sections of the United States (1824), he held teaching positions at the United States Military Academy, West Point, N.Y. (1824–27), the College of Physicians and Surgeons (1827–55), and the College of New Jersey (later Princeton; 1830–54), teaching chemistry, natural history, mineralogy, and geology.

In 1834 Torrey met a student from New York, Asa Gray, who was to become an important botanist. Together they completed materials for A Flora of North America, 2 vol. (1838–43), but the work was interrupted when Torrey became state botanist of New York (1836) and was thus obliged to begin work on his Flora of the State of New York (1843). He amassed one of the most valuable botanical libraries and herbaria in the United States. His collection was given to the New York Botanical Garden in 1899. Torrey's name is commemorated in Torreys Peak in Colorado.