Hill's contract with the club was set to expire at the end of October, reports Bobby Nightengale of the Cincinnati Enquirer.
Miami made the playoffs for the first time since 2003 this year, and the Marlins went on a surprising run to the NLDS. Hill joined the front office in 2002 and was promoted to president of baseball operations in 2013 after serving as general manager for seven years.
The 49-year-old was one of only two Black heads of baseball operations in the majors.
The Marlins registered just one winning season under Hill after he became the team's top executive.
Meanwhile, Miami promoted Dan Greenlee to assistant GM, according to Jon Heyman of MLB Network.