The actor and artist has been appearing in a live video stream called He Will Not Divide Us since President Trump's inauguration on Friday.
The New York Police Department said Mr LaBeouf was involved in a dispute in the early hours of Thursday.
No-one else was charged and Mr LaBeouf has now been released.
During the incident, a 25-year-old man sustained scratches after a verbal confrontation escalated to a physical confrontation, a police spokesman said.
According to TMZ, a member of the public walked in front of the camera and said something the actor objected to.
Mr LaBeouf then allegedly took hold of the man's scarf. Police said he also pushed the man, who refused medical attention.
The actor could be seen in handcuffs walking off with a police officer in the live video stream. He must attend a court hearing on 7 April.
Mr LaBeouf has starred in films including the Transformers franchise, Indiana Jones and the Kingdom of the Crystal Skull and Wall Street: Money Never Sleeps.
He has also become known for his performance art projects in recent years. In the name of performance art, he has answered phone calls from the public in Liverpool, spent 24 hours in a lift in Oxford and wore a paper bag over his head at the Berlin Film Festival.
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