The rocker has filed papers in San Diego County Superior Court, California, according to TMZ.
Tom wed his high school sweetheart, Jennifer, in 2001. They are parents to kids Ava, 17, and 13-year-old Jonas.
The singer has cited "irreconcilable differences" as the reason for the split and lists December 29, 2017, as the date of separation.
He's asking for joint legal and physical custody of the couple's children.