In papers filed in Los Angeles, the 45-year-old cited irreconcilable differences and revealed the couple signed a prenuptial agreement.
Sheen wants joint custody of their twin sons while his wife, who has also filed for divorce, wants sole custody.
Both say in legal papers that they separated after an argument in Aspen, Colorado, on Christmas Day.
A police report, released in August, stated Mueller feared for her life during the argument.
Sheen was sentenced to 30 days at a rehabilitation centre after pleading guilty to assault.
Last week, the actor was accused of causing damage to a hotel room in New York.
After hotel security reported Sheen was disorderly, the actor voluntarily went with authorities for a psychiatric evaluation.
However, Sheen's publicist said he went to hospital because he had "an adverse allergic reaction to some medication".
Sheen's ex-wife, actress Denise Richards, was staying at the Plaza in a different room with their two children, Sam and Lola.
Sheen and Richards divorced acrimoniously in 2006 after four years of marriage.
Two and a Half Men star Charlie Sheen has filed for divorce from his third wife Brooke Mueller.