Marlins principal owner Bruce Sherman said in a statement the club exercised its team option for Ng to return for the 2024 season but that she declined her mutual option.
"We thank Kim for her contributions during her time with our organization and wish her and her family well," said Sherman.
"We will immediately begin a thorough and extensive search for new leadership as we plan to continue to invest in the Marlins organisation both on and off the field."
The announcement comes less than two weeks after Miami, who went 84-78 in the regular season, were swept by the Philadelphia Phillies in the best-of-three National League Wildcard Series.
In November 2020, Ng joined a rebuilding Marlins that were one of MLB's biggest surprise stories that year as they made the playoffs for the first time since 2003.
When Ng was hired by Miami, MLB Commissioner Rob Manfred called it a "significant example" for the millions of women and girls who love baseball and softball.
Prior to joining the Marlins, Ng worked as an executive in the MLB Commissioner's office as senior vice president of baseball operations and previously served as assistant general manager for the New York Yankees and Los Angeles Dodgers.
