Williams was born and raised in Manhattan. His mother was Patricia Agnes Jones, a dancer, and his father is architect Tod Williams of the husband-and-wife architectural firm, Tod Williams Billie Tsien Architects.
Williams studied painting and literature at Bard College and Columbia University before finding work as a stringer for the New York Times, Los Angeles bureau. Next, he attended the American Film Institute.
Williams was married to actress Famke Janssen from 1995 to 2000. He has been married to actress Gretchen Mol since June 1, 2004. Their first child, son Ptolemy John Williams, was born on September 10, 2007. Their second child, daughter Winter Morgan Williams, was born on February 17, 2011. His sister is the model Rachel Williams.