Nixon has two children, daughter Samantha (b. 1996) and son Charles Ezekiel (b. 2002), with Danny Mozes, an English professor, with whom she had a relationship from 1988 to 2003.

Nixon began dating education activist Christine Marinoni in January 2004; media reports of the relationship started surfacing in September of the same year. In February 2005, the New York Post and other sources reported that Nixon had moved to Brooklyn to live with Marinoni. However, Nixon told the The New York Times in January 2006 that she had not moved and that keeping her kids in their Manhattan public schools took priority. Discussing her relationship in an interview in New York Magazine in 2006, Nixon stated that she never felt any struggle with her sexuality: "I never felt like there was an unconscious part of me around that woke up or that came out of the closet; there wasn't a struggle, there wasn't an attempt to suppress. I met this woman, I fell in love with her, and I'm a public figure." I