Cruft's first marriage was to Charlotte Hutchinson in 1878. Together they had four children, Charles Francis, Louise, Cecil Arthur and Clara Helen Grace. His second marriage was to Emma Isabel Hartshorn in 1894, they had no children. He remained in close contact with his children, and involved each of them in the dog show business. Such was the relationship with his daughter Clara, who was nicknamed "Birdie", that she alone was listed in his second wife's will as a step daughter.