Bonham Carter was in a relationship with actor and director Kenneth Branagh in the 1990s. They met while working together and were a notable couple in the entertainment industry. The relationship ended in 1999.

Bonham Carter began a relationship with director Tim Burton in 2001 after meeting on the set of 'Planet of the Apes'. They never married but shared a unique and unconventional relationship, living in adjoining houses in London.

Bonham Carter and Tim Burton welcomed their first child, a son named Billy Raymond Burton.

Bonham Carter and Tim Burton had their second child, a daughter named Nell Burton.

Bonham Carter and Tim Burton announced their separation in December 2014. Despite the end of their romantic relationship, they remained friends and continued to co-parent their children.

Bonham Carter began a relationship with writer Rye Dag Holmboe in 2019. They have been seen together at various events and appear to be in a stable and happy relationship.