Mesenchymal stem cells (MSCs) are increasingly becoming a potential treatment approach for bone injuries due to the multi-lineage differentiation potential, ability to recognize damaged tissue sites and secrete bioactive factors that can enhance tissue repair. The aim of this work was to improve osteogenesis of carbon fibers reinforced polyetheretherketone (CF/PEEK) implants through bone marrow mesenchymal stem cells (BMSCs)-based therapy. Moreover, bioactive graphene oxide (GO) was introduced into CF/PEEK by grafting GO onto CF to boost the osteogenic efficiency of BMSCs. Subsequently, CF/PEEK was implanted into the symmetrical skull defect models of SD rats. Then in vivo biosafety and osteogenesis were evaluated. The results indicated that surface wettability of CF/PEEK was effectively improved by GO, which was beneficial for the adhesion of BMSCs. The pathological tissue sections stained with H&E showed no significant pathological change in the main organs including heart, liver, spleen, lung and kidney, which indicated no acute systemic toxicity. Furthermore, bone mineralization deposition rate of CF/PEEK containing GO was 2.2 times that of pure CF/PEEK. The X-ray test showed that the surface of CF/PEEK containing GO was obviously covered by more newly formed bone tissue than pure CF/PEEK after 8 weeks of implantation. This work demonstrated that GO effectively enhanced surface bioactivity of CF/PEEK and assisted BMSCs in accelerating differentiation into bone tissue, providing a feasible strategy for improving osteogenesis of PEEK and CF/PEEK.