Thompson published numerous books on Vermont's history, the most notable being the History of the State of Vermont (1833) and History of the State of Vermont, Natural, Civil and Statistical (1842).
Thompson married Phebe Boyce and had three children: George Boyce Thompson, Harriet Towner Thompson, and Adeline Perry Thompson. Only his daughter, Adeline, survived childhood; she had four children before her death, at 30.