Dating 2005, they became engaged in 2009

(October 18, 2011 - present) (separated September 2023)

In 2004, Phillips began dating actor Danny Masterson;[24] the couple met at a poker tournament in Las Vegas. They are both Scientologists. The couple announced their engagement in March 2009 and were married in October 2011 in a private castle in Ireland. On February 14, 2014, Phillips gave birth to their daughter. Phillips starred with Masterson in several films and in a 2011 episode of Fox's Raising Hope.

Masterson revealed in February 2017 that Phillips had been suffering from kidney disease for five years. She was born with small kidneys and had been battling the disease by living a stress-free life, eating a vegan diet, and getting dialysis. She suffered from a blood infection and was in need of a transplant. In April 2017, she received a kidney transplant.

After her sister Mackenzie's allegations of sexual assault against their father, Phillips said in 2009, "I'm 29 now, I've talked to everyone who was around during that time, I've asked the hard questions. I do not believe my sister. Our father [was] many things. This is not one of them." Phillips also stated that Mackenzie told her about their incestuous relationship, and that the news was "confusing and scary" and that she was "heartbroken" to think that her family left her alone with her father.[32] In a 2000 interview with Bruce LaBruce, she discussed a song she had written about her father with the refrain, "He touched me wrong", but did not go into detail about whether the lyrics referred to herself or someone else.

Between 2017 and 2020, Phillips’ husband Masterson was accused of rape, harassment, and stalking of several women (including Chrissie Carnell-Bixler, the wife of musician Cedric Bixler-Zavala). In September 2023, Masterson was sentenced to 30 years to life in prison. Later that month, she filed for divorce.