Motivated by the success of using graphene oxide (GO) as a nanofiller of composites, there is a drive to search for this new kind of carbon material as a reinforcing phase in biocomposites. In the present work, graphene oxide and chitosan (CS) functionalized graphene oxide were introduced as templates to fabricate hydroxyapatite (HA) using a facile solution-based in situ synthesis method, and GO–HA and CS-GO–HA nanocomposites were successfully prepared for the first time. It was found that the spindle like HA nanoparticles with a diameter of about 27 ± 7 nm and a length around 150 ± 25 nm were decorated randomly and strongly on the surface or aggregated at the edges of the pristine and chitosan functionalized GO matrix. Compared with HA, the prepared GO-based HA nanocomposites displayed an increased elastic modulus and hardness. The in vitro cytotoxicity of the prepared nanocomposites was investigated using CCK-8 assay on murine fibroblast L-929 cell line and human osteoblast-like MG-63 cell line, respectively. Both of the nanocomposites exhibited a high cell proliferation rate for L-929 and MG-63, and the CS-GO–HA could provide significantly higher cell viability and alkaline phosphatase activity compared to the GO–HA composite. These findings may provide new prospects for utilizing the GO-based hydroxyapatite biocomposites in bone repair, bone augmentation, as well as coating of biomedical implants and broaden the application of GO sheets in biological areas.