According to court documents obtained by ET, the 38-year-old actress is seeking spousal support, as well as joint legal and physical custody of their two sons - 12-year-old IN and 9-year-old Atticus.
The couple first announced their separation in March of 2016, putting an end to a Hollywood relationship that spanned 16 years.
According to divorce papers filed by the "the Believer" actress, the couple actually separated in November 2015 due to irreconcilable differences and Phoenix has requested joint physical and legal custody of the children according to TMZ.
Neither has commented publicly on the divorce filing. The two separated after more than 13 years together.
An earlier report from In Touch magazine suggested that Summer was having trust issues when the reports surfaced that her husband of nearly ten years was having an affair.
Casey Affleck and Summer Phoenix at the premiere of The Killer Inside Me " in New York, April 27, 2010. Both suits were settled out of court.