He was married to Susannah Hayward of Bridgewater, Massachusetts. They had six children. However only two daughters lived into adulthood.
Thacher was stationed at West Point in 1780 and supported the execution by George Washington of the British spy John André. He was the author of Military Journal during the American Revolutionary War (1823); Observations Relative to the Execution of Major John André as a Spy in 1780 (1834); American New Dispensatory (1810; fourth edition, 1821); and other books.