As one of the promising orthopedic materials, polyetheretherketone (PEEK) has high chemical durability and similar mechanical properties to the cortical bone; nevertheless, the inherent bioinert nature of PEEK dramatically impedes its broader clinical applications in the management of bone infection. To address this challenge, herein, we developed a multifunctional two-dimensional (2D) nanocoating to assemble graphene oxide (GO) nanosheets, a polydopamine (pDA) nanofilm, and an oligopeptide onto the surface of porous sulfonated PEEK (SPEEK). The resulting multifunctional PEEK implants exhibited enhanced cytocompatibility, alkaline phosphatase activity, and calcium matrix deposition as well as osteogenesis-associated gene expression. Moreover, the animal experiments based on a rabbit femur defect model confirmed that the 2D nanocoating prominently boosted the in vivo osseointegration and bone remodeling. Besides, the GO/pDA hybrid complex anchoring on the SPEEK surface through π-π stacking can generate robust antibacterial phototherapy resulting from the synergetic photothermal/photodynamic therapeutic effects. Accordingly, this work provides a paradigm to empower inert PEEK implants with bi-/multi-modal therapeutic applications, such as against bone infection treatment.