James Thornton was born on his family's plantation, Fall Hill, in Fredricksburg, Virginia. He was the son of Francis and Sarah Innes Thornton. James was educated at Washington College ( now Washington & Lee University ) and migrated to Huntsville, Alabama following graduation. He practiced law in Huntsville in 1820. He was elected Alabama's third Secretary of State in 1824. He was 24 years old. He remained in this position until 1834.

He then retired from public life and became a planter in Greene County, Alabama. He developed Thornhill Plantation which consisted of over 2,600 acres and was worked by over a 150 slaves.

James was a distant relative of President George Washington. Mildred Washington Gregory was George Washington's paternal aunt. She had three daughters who married three Thornton brothers. Her daughter Frances married Colonel Francis Thornton III of Fall Hill. They were the great grandparents of James Innes Thornton.

James was also the uncle of Lieut. James Fitzgerald Forbes who was killed on May 4, 1863 in the same volley of shots that fatally wounded Confederate General Thomas Stonewall Jackson. Forbes was the son of James's sister, Sally Innes Thornton Forbes and her husband Murray.

James was married 3 times. His first wife was Mary Amelia Glover Thornton who he married on January 3, 1827. They had two daughters. Mary died on May 25, 1830 in Tuscaloosa, Alabama at the age of 21 years and 5 months. She is buried in Demopolis, Alabama in the Glover Mausoleum in Riverside cemetery. He married his second wife in 1830 and they had 9 children. Anne Amelia Smith Thornton died on August 2, 1864 and is buried with James in Thornhill cemetery. He married his third wife Sarah Williams Gould Gowdy Thornton ( June 11, 1824 - August 23, 1885 ) in 1870. She is buried in the Bethsalem Cemetery in Boligee, Alabama.

During the American Civil War, James was philosophically opposed to the doctrine of succession of the southern states. He also argued against the glory in the sacrifice of the south's young men. Nevertheless he supported "The Cause " financially.

James died at home, only weeks short of his 77th birthday. He was buried in the Thornton family cemetery at Thornhill.