The death of his father called him home and he took charge of the farm, occasionally preaching in the neighborhood churches, 1778-83. At the same time he conducted a day school and while New Haven was in the hands of the British, he had under his care several of the refugeed Yale students. He was a representative in the Massachusetts legislature, 1782, and refused a nomination as representative in congress. He was pastor of the church at Greenfield Hill, Fairfield, Conn.,1783-95, and established there his celebrated academy and became the pioneer of higher education of women, placing both sexes on an equal footing in his school. During this period he secured the union of the Congregational and Presbyterian churches in New England.

He was president of Yale college from Sept. 8, 1795, to Jan. 11, 1817, and Livingston professor of divinity pro tempore, 1795-1805, and by election, 1805-1817. He found the college with a narrow and pedantic curriculum, with the bitterest of feeling existing between the freshmen and the upper-class men, and between the students and the faculty, and with the burden of a primary system. These he reformed, and at his death the 110 students had increased to 313 and the college had taken rank as one of the model university schools in America.

He was married in March, 1777, to Mary, daughter of Benjamin Woolsey of Long Island and they had eight sons, the eldest of whom, Timothy (1778-1884), was a merchant in New Haven and gave $5000 to endow the Dwight professorship of didactic theology at Yale. He received from the college of New Jersey the degree of S.T.D. in 1787, and from Harvard that of LL.D. in 1810.