In papers filed on Thursday in New York, the actress, 33, is seeking "primary residential custody" of their 6-year-old daughter, Suri, according to TMZ.com.
Holmes cites the standard "irreconcilable differences" for the end of their five-year marriage and wants a "suitable amount" of child support from the 49-year-old star, TMZ reports.
Cruise's rep issued a statement confirming that it was Holmes who filed for divorce and saying the Rock of Ages star is "deeply saddened."
The pair were married in November 2006 in Italy. Holmes and Suri were last spotted Thursday outside their home in New York, and Cruise has been on location in Iceland filming Oblivion.