On 6 April 1793 in Washington ,Georgia. Thompson married Eliza Blackburn Williams, daughter of James Williams (D. 1794) and Elizabeth Blackburn. They were the parents of twelve children: ELiza Williams (M. Robinson M Earle), Maria Swann (M. Richard Harrison), Waddy Jr. Sarah Williams (M. 1st Harvey Cleveland, 2nd James Williamson Quarles), Emily C. (M. Thomas F Jones), James Williams, James THomas, Caroline Eliza (M. Robert Alexander Means), Henry Tazewell, Theodore Blackburn, Thomas Williams, and Cornelia Eugenia (m. Ralph Armstrong). Eliza Blackburn Williams Thompson predeceased her husband 30 January 1830. Wady Thomspon died 9 February 1845 in Greenville.