On 23 December 1593, Jones married Sarah Twitt, the daughter of a fairly wealthy Harwich merchant. She lived across the street from Jones in Harwich. Within a year of their marriage in St. Nicholas's Church, Harwich, they had a son, Thomas. The boy was baptized on 1 December 1595. He died a few months later on 17 April 1596. Sarah's father died in 1599, leaving Christopher and Sarah Jones a twelfth share in the ship "Apollo". Sarah died in 1603. She was buried on 23 May 1603 in Harwich.