Investigators said the two men accosted the 49-year-old victim as they all rode the northbound A train at 3:35 a.m. Wednesday.
For unknown reasons, the men started using anti-Muslim names and slurs.
The verbal abuse then turned physical, police said, with the two men ganging up on the Imam.
The fight spilled onto the Canal Street station platform, and the Imam was pushed to the ground.
He suffered minor bruises, but refused medical attention.
Police arrested 30-year-old Albert Melendez of Harlem and 28-year-old Eddie Crespo of Staten Island.
They are charged with assault as a hate crime and related offenses.