Thomas Morris practiced law at Canandaigua, New York, and managed business connected with his father Robert Morris's western land investments. His work placed him at the intersection of settlement, speculation and negotiations with the Seneca Nation. In 1797 his father empowered him and Charles Williamson to acquire Seneca rights to a vast tract west of the Genesee River, land promised to investors in the Holland Land Company.

Morris helped conduct the negotiations remembered as the Treaty of Big Tree. Seneca leaders resisted surrendering their territory, and the agreement reserved separate tracts for their communities. In exchange for the larger cession, Robert Morris undertook to place $100,000 in bank stock for the nation. Thomas acted as his father's agent, rather than as the federal commissioner supervising the proceedings. The transaction opened much of western New York to outside ownership while sharply reducing the Seneca land base.

Morris also represented his district in the New York Assembly from 1794 to 1796. Elected as a Federalist to the United States House, he served from March 1801 to March 1803 and did not seek renomination. He then moved his law practice to New York City. Appointed United States marshal for the Southern District of New York in 1816, he received further appointments in 1820, 1825 and 1829. His surviving correspondence concerns both public affairs and personal business. He continued living in New York, where he died in March 1849.