Thomson is the father of six children from four different mothers. With his first wife, Mary Lou La Prairie, he has two daughters: Thyra Nicole and Tessa Lys. With his second wife, Laurie Ludwick, Thomson has one son, Benjamin, born after Thomson left the marriage. With the actress Kelly Rowan, Thomson has a daughter. With his partner Severine Nackers, an employee of Sotheby's in London, Thomson has two daughters, Ottilie, born in 2015, and Elodie, born in 2018. His two youngest children live with their father and mother. Thomson was estranged from his eldest daughter, Thyra, for five years, with Thyra eventually suing her father over mismanagement of the family trusts. The case was settled out of court in 2017. Thomson lives alone in a private residence that also houses an underground art gallery, in Rosedale, Toronto. Three of his children live in London, UK, where Thomson retains several homes.