The San Jose Mercury News reports prosecutors filed the charges lateWednesday against Logan Beaschler and Collin Warren, both 18, and 19-year-old Joseph Bomgardner.
They each face up to a year in jail if convicted.
Authorities say the harassment began in August after the students moved in together. The victim's parents saw the Confederate flag and a dry-erase board with the racial epithet and reported it to housing officials.
University spokeswoman Pat Lopes Harris said the incident is still under investigation. No decision has been made on whether the students will be sanctioned.