Thomas Martyn was the son of the botanist John Martyn (1699–1768). He was educated in Chelsea and at Emmanuel College, Cambridge, graduating BA in 1756 and becoming a fellow of Sidney Sussex College and being ordained deacon in 1758. In 1759 he became MA and priest. In 1762 he succeeded his father as Professor of Botany at the University, and held the post until his death in 1825, though he only lectured until 1796 'as the subject was not popular'. Thomas Martyn's professorship at Cambridge lasted for 63 years, while his father had held the same post for 29 years. Thomas Martyn was elected a Fellow of the Royal Society in 1786.
Two of Martyn's major works are Plantæ Cantabrigiensis (1763) and Flora Rustica, 4 vols. (1792–1794). He translated the Lettres sur la botanique of Rousseau. As a priest in the Anglican church Thomas Martyn preached until he was eighty-two years old; in 1830 George Cornelius Gorham, his curate, published a dual biography consisting of additions to Martyn's memoir of his father and Martyn's autobiographical memoir (Memoirs of John Martyn, F.R.S., and of Thomas Martyn, B.D., F.R.S, F.L.S., Professors of Botany in the University of Cambridge, London, Hatchard & Son). Thomas Martyn's other written works include: The English Connoisseur (1766); The Gentleman's Guide in his Tour through Italy (1787); The Language of Botany (1793); and The Gardeners' and Botanists' Dictionary (1807).