[1] His sister Mary Thomson married William Tucker, a merchant and one of the first plantation owners in the Colony of Virginia.
In the early 1650s, Thomson and business associate Rowland Wilson had engaged James Pope to act as agent on their ship Friendship, for a number of slaving voyages to Gambia.
Dresser quotes them as instructing Pope to, along with loading the ship with African slaves for Barbados, "find 15 or 20 many lusty young Negers and bring them home with you for London".
[2] Thomson married Dorothy Vaux, daughter of John Vaux, of Pembrokeshire, by whom he had children including John Thompson, 1st Baron Haversham (c. 1648 – 1710), eldest son and heir; and Mary Thomson, who became the wife of William Owfield (1623–1664), MP.
He owned estates and property including Elsham, Lincolnshire, which manor he purchased in 1655, and Worcester House, Mile End Green, which he sold in 1675 to the Church.