The actor, 54, and Leoni, 48, are divorcing after 17 years of marriage, a source confirms to PEOPLE, adding that the two have been separated for months.
According to TMZ, the divorce papers were filed in June and cite “an irretrievable breakdown” as the cause of the split.
The former couple will reportedly share joint legal custody of their two children, son Kyd Miller, 12, and Madelaine West, 15, but Leoni will have primary physical custody, with Duchovny paying $8,000 a month in child support, as well as $40,000 a month in spousal support.
He will also reportedly be responsible for all other expenses relating to their kids, including summer camps, private school and college.
After their initial separation in 2008, the same year he entered rehab for sex addiction, Duchovny and Leoni reconciled, later separating for a second time in 2011.