A non-volatile data storage system including a first non-volatile storage medium, a second non-volatile storage medium, and a microprocessor is provided. The first non-volatile storage medium includes a popular data address recording area for recording logic addresses of popular data in the first non-volatile storage medium. The microprocessor is coupled to the first non-volatile storage medium and the second non-volatile storage medium. When the non-volatile data storage system boots up, the microprocessor copies the popular data from the first non-volatile storage medium to the second non-volatile storage medium according to the popular data address recording area. The popular data is accessed in the second non-volatile storage medium instead of the first non-volatile storage medium.