The actress and model -- who is also the younger sister of Affleck's friend and collaborator Joaquin Phoenix -- cited irreconcilable differences in the petition she filed with the Superior Court of California in Los Angeles on Monday.
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 Indiana and 9-year-old Atticus.
The couple, who tied the knot in 2006, separated in November 2015, after being together for over 16 years, according to papers filed with the court. They subsequently announced their split in March 2016.
Apart from spousal support, Phoneix asked the court in her divorce petition for Affleck, 41, to pay for her legal fees, and requested that court terminate her ex's ability to be awarded spousal support.
In March, Affleck's rep confirmed to ET that the couple had split up, stating, "Casey and Summer have amicably separated. They remain very close friends."
Affleck and Phoenix were first introduced in 2000 by her famous older brother, and the pair soon began dating. They welcomed Indiana in May 2004, then exchanged vows at a ceremony in Savannah, Georgia, in June 2006. They welcomed Atticus in January 2008.