Carbon/carbon composite (C/C), due to its bio-inert property, is prone to cause bone consolidation defects and bacterial infections in clinical applications. Therefore, there is a great demand in practical applications to prevent implant infections and enhance its bone consolidation capability. In this study, we have developed a facile approach to construct a chitosan/hydroxyapatite composite modified layer on C/C surface by electrochemical deposition and a covalent grafting technique, and the modified layer has both the antibacterial activity of chitosan (CS) and the bioactivity of hydroxyapatite (HAP). The microstructure and chemical composition of the modified layer were analyzed using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and water contact angle measurements. The biological properties of the composites were evaluated using cell culture, antimicrobial test and real-time quantitative PCR in vitro. The results showed that the CS/HAP modified C/C exhibited excellent biocompatibility, bacteriostasis and osteoinductive ability. These properties are beneficial for the potential application of the modified C/C composite as a bone tissue replacement material.