Cops nabbed a man who allegedly raped his girlfriend’s 9-year-old daughter and subjected her to a mock crucifixion in a Bushwick building.

Phillip Payne, 29, was arrested Thursday afternoon for assaulting the youngster in his home on Knickerbocker Avenue between Dec. 23 and Dec. 30, court papers charge.

Payne entered the girl’s bedroom while she and her siblings were sleeping, pulled down her clothing and raped her “on several occasions,” according to the criminal complaint. When the girl complained of pain and told Payne to stop, he told her, “shhh” before leaving the room, the complaint says.

Payne is also accused of ordering the girl and her brother to stand against the wall as he duct-taped their arms and pressed nails into their hands — imitating a crucifixion — as a form of punishment.

If they dropped their arms, he would hit or pinch them, the court papers say.

Payne was hit with multiple counts of rape, assault, sexual abuse and endangering the welfare of a child, among other charges.

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