Throughout much of his career, he was a teacher of chemistry, often at multiple universities, while he also pursued botanical work,[1] focusing on the flora of North America.

He found the medical profession uncongenial, and on August 5, 1824, he entered the United States Army as an assistant surgeon and became acting professor of chemistry and geology at West Point military academy.

[4] He was frequently consulted by the treasury department on matters pertaining to the coinage and currency, and was sent on special missions at various times to visit the different mints.

Besides being the last surviving charter member of the Lyceum of Natural History, he held its vice presidency for several years, and was president in 1824–26 and 1838, holding the same office in the American Association for the Advancement of Science in 1855, and he was one of the original members of the National Academy of Sciences of the United States, being named as such by act of the United States Congress in 1863.

[3] Torrey died at his home in New York City on March 10, 1873; he was buried in the family plot at Long Hill Cemetery, Stirling, New Jersey.

During the same year, he received the collections made by Edwin James while with the expedition that was sent out to the Rocky Mountains under Major Stephen H. Long.

Torrey, in the meantime, had planned A Flora of the Northern and Middle United States, or a Systematic Arrangement and Description of all the Plants heretofore discovered in the United States North of Virginia, and in 1824 began its publication in parts, but it was soon suspended owing to the general adoption of the natural system of Antoine Laurent de Jussieu in place of that of Carl Linnaeus.

In 1838, he began with Asa Gray The Flora of North America, which was issued in numbers irregularly until 1843, when they had completed the Compositae, but new botanical material accumulated at such a rapid rate that it was deemed best to discontinue it.

[3] Subsequently, Torrey published reports on the plants that were collected by John C. Frémont in the expedition to the Rocky Mountains (1845), those gathered by Major William H. Emory on his reconnaissance from Fort Leavenworth, Kansas, to San Diego, California (1848), the specimens secured by Captain Howard Stansbury on his expedition to the Great Salt Lake of Utah (1852), the plants collected by John C. Frémont in California (1853), those brought back from the Red River of Louisiana by Captain Randolph B. Marcy (1853), and the botany of Captain Lorenzo Sitgreaves's expedition to the Zuni and Colorado Rivers (1854), also memoirs on the botany of the various expeditions for the purpose of determining the most practicable route for a Pacific Railroad (1855–1860).

[3] Torrey's name is commemorated in the small coniferous genus Torreya, found in North America, China and Japan.