In 1824, he was elected to the Legislative Assembly of Upper Canada as a moderate reformer; he was reelected in 1828 and 1830. He supported the freedom of the press, opposed the control of the clergy reserves by the Church of England and supported granting the same rights as British subjects to American-born settlers in Upper Canada. With the replacement of Sir Peregrine Maitland by Sir John Colborne as lieutenant governor, Thomson began to support the government's positions in the legislative assembly.
In 1824, he was elected to represent Upper Canada in the Legislative Assembly as a moderate reformer; he was reelected in 1828 and 1830. He supported press freedom, opposed Church of England control over clergy reserves, and advocated for equal rights for American-born settlers in Upper Canada. Following Sir Peregrine Maitland's replacement by Sir John Colborne as lieutenant governor, Thomson began supporting the legislative assembly.