Bone damage as a consequence of disease or trauma is a common global occurrence. For bone damage treatment - bone implant materials are necessary across three classifications of surgical intervention (i.e. fixation, repair, and replacement). Many types of bone implant materials have been developed to meet the requirements of bone repair. Among them, polyether ether ketone (PEEK) has been considered as one of the next generation of bone implant materials, owing to its advantages related to good biocompatibility, chemical stability, X-ray permeability, elastic modulus comparable to natural bone, as well as the ease of processing and modification. However, as PEEK is a naturally bioinert material, some modification is needed to improve its integration with adjacent bones after implantation. Therefore, it has become a very hot topic of biomaterials research and various strategies for the modification of PEEK including blending, 3D printing, coating, chemical modification and the introduction of bioactive and/or antibacterial substances have been proposed. In this systematic review, the recent advances in modification of PEEK and its application prospect as bone implants are summarized, and the remaining challenges are also discussed.