Naya cites irreconcilable differences for ending her 3-year marriage to the actor.

In her legal docs, filed by "Disso Queen" Laura Wasser, she's asking for joint custody of 2-year-old Josey. She also wants the court to block either of them from getting spousal support.

Naya previously filed for divorce in November 2016 but later dismissed it.

Sources tell us the arrest over Thanksgiving weekend was the last straw for her. As TMZ reported, Naya was arrested Nov. 25 for domestic battery after allegedly hitting Ryan in the head over a dispute involving their son. Interestingly, she lists the date of separation as Nov. 24.

Our sources say it's not the first time the police got involved in their marriage. We're told Naya called the cops on Ryan 3 times during their marriage.