To improve the performance of polyether ether ketone matrix (PEEK) in hard tissue repair and replacement applications, we fabricated graphene (G) reinforced PEEK with graded G concentrations (0.1%-5%) through injection molding. The mechanical properties, surface morphology, chemical composition and thermal stability of the composites have been characterized through universal mechanical testing, scanning electron microscopy, contact-angle measurement, transmission electron microscope, X-ray photoelectron spectroscopy, X-ray diffraction and thermal analysis system. The biocompatibility has been assessed in vitro and the bone repair function of the composite implant have been assessed in vivo using a rabbit mandibular bone defect model. Mechanical testing results suggest that the composite samples have compressive moduli similar to that of the natural bone. Although addition of G into PEEK does not significantly influence the composite tensile, flexural or compressive moduli, it can significantly enhance the ductility and toughness of the material. On the other hand, all G-reinforced PEEK implants demonstrated enhanced adhesion and differentiation of rat bone marrow stromal cells (BMSCs), with 5% G-PEEK showing the highest bioactivity among all samples. The in vivo osseointegration data further revealed that 5% G-PEEK has the best effect in promoting osseointegration and bone regeneration, in both early stage and late stage bone re-growth. Study shows that our G-reinforced PEEK-based implants provides a promising strategy for enhancing the performance of future regenerative bone implants.