Background
He was the eldest son and heir of Robert Thomson of Watton-at-Stone, Hertfordshire, by his wife Elizabeth Harsflet, daughter of John Harsflet (alias Halfehead, Harsnett) of Watton-at-Stone. His sister Mary Thomson married William Tucker, a merchant and one of the first plantation owners in Virginia. His younger brothers included:
Colonel
George Thomson(c1607–1691), a merchant, Parliamentarian soldier and Member of Parliament for Southwark.
Robert Thomson, youngest brother, a merchant.
Paul Thomson
Sir William Thomson.