He was born in Ireland: his family emigrated to America when he was three years old, settling first at Wiscasset, Maine, and removing shortly thereafter to Worcester, Massachusetts. Thornton became a physician and was appointed surgeon to the New Hampshire troops in the expedition against Louisburg. He had royal commissions as justice of the peace and colonel of militia. He became Londonderry Town Selectman, a representative to, and President of the Provincial Assembly, and a member of the Committee of Safety, drafting New Hampshire's plan of government after dissolution of the royal government, which was the first state constitution adopted after the start of hostilities with England.
He was first President of the New Hampshire House of Representatives and Associate Justice of the Superior Court of New Hampshire. He was elected to the Continental Congress after the debates on independence had occurred, arriving just in time to actually sign the Declaration of Independence.
He became a political essayist. He died in Newburyport, Massachusetts, while visiting his daughter.