In the court papers, Witherspoon, 30, asks for joint custody of the couple's two children, Ava, 7, and Deacon, 3. The actress also seeks physical custody of her kids and that Phillippe, 32, be granted visitation rights.
Witherspoon also requests that the court not grant spousal support for Phillippe.
A rep for the couple first announced their separation on Oct. 30.
Though Phillippe hasn't commented on reports that he and Australian actress Abbie Cornish (who costars with him in an upcoming film) had a relationship, he issued an exclusive statement to PEOPLE on Wednesday, saying, "I'm not a perfect person, but I’m not guilty of a lot of the things I have been accused of. My priority is and always has been the health and safety of my family." Reps vehemently deny other allegations of hard partying and drug use.
Witherspoon, who won an Oscar for her role in last year's hit Walk the Line, is next expected to appear in the drama Rendition. Phillippe is currently starring in the WWII drama Flags of Our Fathers.