The documents indicate that Julianna Zobrist, a professional singer, is the plaintiff. Ben Zobrist, 37, is in the final season of a four-year contract with the Cubs.
Zobrist was granted a leave of absence a week ago. He is hitting .241 with 10 RBIs in 26 games this season.
Julianna Zobrist did not provide a reason for seeking a divorce in her petition, which was filed Monday. The two married in December 2005 and have three children.
The Cubs have not given any indication when Zobrist is expected to be back.
"I texted with him the other day and reminded him how much I care about him, how much we miss him," Cubs manager Joe Maddon said, according to ESPN.