Marilyn Manson sexually assaulted a 16-year-old in his tour bus and threatened to kill her family if she spoke out, a new lawsuit alleges.

A woman — who filed suit anonymously under the name Jane Doe — claims that the shock rocker sexually assaulted and raped her many times from 1995 through 1999, beginning a few days after her 16th birthday on Sept. 15, 1995, according to the lawsuit filed Monday in New York’s Nassau County Supreme Court.

The now-44-year-old accuser also brought claims against Manson’s record labels Interscope Music and Nothing Records — the latter founded by Nine Inch Nails rocker Trent Reznor — claiming they promoted and profited off Manson’s sexual deviance, including an apparent penchant for pedophilia, the filing claims.

The labels “were well aware of [Manson’s] obsession with child pornography and pedophilia and his desire to expose children across America to sexual themes,” the suit charges. The labels promoted this “for added publicity and financial gain,” the court papers allege.

Doe — who lived in Maryland at the time — says that after the show, she and a group of other young girls waited outside Manson’s tour bus, but he only invited Doe and another girl in. She claims he asked them detailed questions about their ages, where their parents were and even jotted down their phone numbers and addresses.

Then, while on the bus, Manson — whose real name is Brian Warner — “performed various acts of criminal sexual conduct upon Plaintiff, who was a virgin at the time, including but not limited to forced copulation and vaginal penetration,” all while another bandmate was watching, the filing alleges.

When Manson, 54, was done, he told her to “get the f–k off of my bus” before threatening to kill her family if she spoke about what happened, the court papers claim.

Doe “was in pain, scared, upset, humiliated and confused,” and soon after the incident developed a drug and alcohol addiction, the suit claims.

Weeks later, Manson contacted her at her home, asking her to send racy photos of herself and her friends to his fan club Satan’s Bakesale, the suit claims. And he spoke to her through an internet chat group, getting her to come to another performance in New Orleans, Louisiana, on Dec. 9, 1995, the court papers say.

There, Manson “groomed Plaintiff by complimenting her, playing with her hair and looking at the photos and drawings she brought with her,” before again sexually assaulting her, the suit claims.

Doe claims she was also sexually assaulted by Manson many times over the course of a month while he was on tour, years later in 1999 when she was 19 years old, according to the suit.

Manson was engaged to “Charmed” actress Rose McGowan from 1997 to 2001.

“Plaintiff was lured into Defendants’ dark world of drugs, alcohol, sexual deviance, harassment, abuse and assault,” the suit charges.

During this period, Manson and “his associates” gave her drugs and alcohol and he was able to continue his abuse of her as an adult because of his prior grooming of her when she was still a minor, the suit claims.

“[Manson] coerced her to have sex with him. [Manson] often coerced Plaintiff to have sex with him and other band members or his assistant at the same time,” court papers charge.

During this time, she claims Manson was very controlling of her and it even turned “hostile and verbally abusive,” the suit claims.

In 2021, women began coming forward with allegations of abuse against Manson, prompting Doe to come forward online. She says Manson retaliated against her, including by revealing sensitive information about her, hacking her online accounts and harassing her through various websites, the court papers allege.

Doe is suing for unspecified damages.

“Brian Warner and his promoters are now held to answer for decades of decadence, violence, predation, and intimidation,” Doe’s lawyer Jeff Andersen said in a statement.

Manson’s lawyer Howard King said his client doesn’t know Doe and was “never intimate with her.”

The lawyer said that Doe’s story keeps changing and called her lawsuit “a shakedown” that’s filled with “vicious lies.”

“She has been shopping her fabricated tale to tabloids and on podcasts for more than two years,” King said. “But even the most minimal amount of scrutiny reveals the obvious discrepancies in her ever-shifting stories as well as her extensive collusion with other false accusers.”

“The remarkable inconsistencies will demonstrate why this misguided action will not survive legal examination,” King said.

“Brian will not submit to this shakedown – and the courts won’t fall for it either.” Universal Music Group — the parent company of Interscope and Nothing Records — didn’t immediately return requests for comment.

But in an Instagram post from 2021, Manson said: “My intimate relationships have always been entirely consensual with like-minded partners.”

At least 15 women have accused Manson of sexual, psychological and physical abuse — including “Westworld” actress Evan Rachel Wood. Manson and his lawyers have denied the allegations.

“Game of Thrones” actress Esmé Bianco filed suit against the musician in 2021, claiming he drugged, tortured and sexually assaulted her. Manson has also denied those allegations. The case was settled last week, court records show.