The actress filed papers to end her marriage to the Manchester by the Sea actor on Monday.
The couple initially revealed the end of their marriage in March 2016.
Summer, the younger sister of famed actors River and Joaquin Phoenix, requested joint physical and legal custody of their children, as well as spousal support, according to E! News.
The couple have a 13-year-old daughter, India Affleck, and a nine-year-old-son, Atticus Affleck.
She cited irreconcilable differences as the reason for the split from Affleck.
They met in 1995 when Phoenix's brother Joaquin introduced the two. They tied the knot in 2006. They have not appeared in public together since 2014.
As Radar previously reported, Affleck was once sued by two former female employees for allegedly sexually harassing them on set. The parties eventually settled out of court.
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