According to the documents, which were filed Monday in Los Angeles, Sheen cited irreconcilable differences, stating the couple separated last Christmas, when the 45-year-old actor was arrested on assault charges.
Sheen and Mueller, his third wife, were married in May 2008. They have twin sons. Sheen is seeking joint custody.
The split comes less than a week after the Two and a Half Men actor was hospitalized in New York. His rep told TVGuide.com that Sheen suffered an "adverse allergic reaction" to medication, though a law enforcement official told the AP that Sheen checked himself into a hospital for a psychiatric evaluation after a woman told police he threw furniture in his hotel room.
In August, Sheen was ordered to 30 days in rehab after pleading guilty to third-degree domestic violence stemming from his Christmas Day dispute with Mueller.
Reps for Sheen did not immediately respond to TVGuide.com's request for comment.