A migrant staying at a Manhattan mega-shelter was busted for allegedly pummeling his wife as she held her toddler son Thursday night — the latest instance of domestic violence among asylum seekers in the Big Apple, police sources said.

Christopher Aquillon allegedly punched his 33-year-old wife in the face around 10:40 p.m. on Thursday while demanding her cell phone inside the shelter on Third Avenue near East 97th Street in Carnegie Hill, a former student housing complex, according to the sources. 

The wife – who was holding her 2-year-old son at the time – complied, but Aquillon, 38, allegedly punched her a second time as he looked through her phone, the sources said. 

The woman suffered a cut on her forehead and walked into the 23rd Precinct to report the incident, according to the sources. 

Cops called Aquillon to come to the station house, where he was cuffed, the sources said. 

The shelter was intended to house more than 500 families with kids, Mayor Eric Adams said in late June.

Sources told The Post earlier this week that at least 41 people have been arrested at the Roosevelt Hotel since the city turned the former swanky Prohibition-era Midtown East hotel into a migrant shelter in May. 

Most of the alleged crimes stemmed from domestic violence incidents, law-enforcement sources said Sunday.

And on Thursday, six residents of a Brooklyn migrant shelter were arrested — three of them for assault on an officer — for allegedly getting rowdy during an NYPD crackdown on illegal scooters, sources said.

Cops showed up at the men’s shelter at 455 Jefferson Street in East Williamsburg after the department got several complaints from the community about mopeds, scooters, and bikes parked in the area.

Some of the residents got out of hand when cops began confiscating the vehicles, sparking a scuffle that led to the arrests, law enforcement sources told The Post.