Bijou Phillips was born in Greenwich, Connecticut, to John Phillips of the Mamas and the Papas and his third wife, Geneviève Waïte, a South African model, artist, and actress.

After her parents split up, both were found unfit to have custody of Bijou, and she was placed in foster care with a family in Bolton Landing, New York. Her father won custody when she was in third grade.

Bijou's half-sister Mackenzie informed her of Mackenzie's ten-year incestuous relationship with their father, which had a devastating effect on Bijou's teenage years.