Polyetheretherketone (PEEK) is an alternative biomedical polymer material to traditional metal and ceramic biomaterials. However, as a bioinert material, its wide application in the medical field is seriously restricted due to its lack of bioactivity. In this research, pure Mg was successfully deposited on a PEEK substrate by vapor deposition to improve the antibacterial properties of PEEK implants. The morphology and elemental composition of the coating were characterized by scanning electron microscopy (SEM) and energy-dispersive spectroscopy (EDS). The higher the deposition temperature, the larger the Mg particle size. The Mg coating possesses a hydrophilic surface and a higher surface free energy that create its good biocompatibility. The Mg coating on a PEEK substrate withstands up to 56 days’ immersion. The antibacterial test showed that the antibacterial rate of coated PEEK is 99%. Mg-coated PEEK demonstrates promising antibacterial properties.