To evaluate the biomechanical properties and biocompatibility of natural hydroxyapatite/chitosan (HA/CS) composites. The natural HA/CS composites with a different proportion of HA and CS were prepared by the cross-linking method, and then the compressive strength, microstructure and pH values of extracts from these composites were measured by SEM and pH meter, respectively. Subsequently, the biocompatibility of the composites was evaluated by means of a series of biological tests, including MTT, acute systemic toxicity, heat source, and hemolysis tests in vitro. The chitosan content in the composites had significantly influenced the mechanical properties and microstructure of the composites. The pH value of the composite extract was approximately 7.0, which was very close to that of human plasma. Furthermore, the natural HA/CS composites showed no cytotoxicity, irritation, teratogenicity, carcinogenicity and special pyrogen. These results indicated that the natural HA/CS composite may be a potential bone repair material.