The 76-year-old Anderson tells The Clarion-Ledger that he and wife intend to travel, play golf and spend time with their grandchildren.
Anderson compiled an 11-18 record this past season. The Canton, Miss., native was the head coach at Murray State before coming to JSU and was a long-time assistant coach at Auburn and Georgia before working at Murray State.
Anderson led Jackson State to the NCAA Tournament in 2007, where the Tigers lost to Florida in the opening round.
Overall, his record at Jackson State was 149-170.
Jackson State will now look for its first coach since 2003 when Anderson replaced Andy Stoglin.