Caullery taught at the University of Marseille (1900) and the University of Paris (1903) and succeeded Alfred Giard as director of the zoological station at Wimereux (1909). He was particularly interested in how the morphology, reproduction, and ecology of tunicates (related to vertebrates) and annelid worms had a bearing on their evolution. He also described and named the marine worm Siboglinum weberi, which later became the basis for establishing the invertebrate phylum Pogonophora.

Among Caullery's more important works are Le Parasitisme et la symbiose (1922; Parasitism and Symbiosis, 1952), Le problème de l'évolution (1931; “The Problem of Evolution”), and Organisme et sexualité (1942; “Organism and Sexuality”).