Graffiti reading "Vote Trump" was also sprayed on the side of Hopewell MB Church in Greenville.
Fire Chief Rueben Brown told Associated Press that the kitchen and auditorium received "substantial" damage before firefighters were able to put out the blaze at around 9.00pm. There were no injuries.
Police officials said they were interviewing a person of interest and investigating the incident as a hate crime.
Pastor Carolyn Hudson told a press conference that The church has a 111 year history and the act had left "our hearts broken."
Over $144,000 has been raised for repairs of the church on the crowdfunding website Gofundme so far. Donations have come in from people on both sides of the political divide.
The attack comes a week before the US presidential election.