As alternatives to autografts, allografts, and xenografts, calcium phosphate (CaP)-based bone-defect-filling materials (e.g., deproteinized bovine bone (DBB, Bio-Oss ® )) are widely used to repair large-volume bone defects (LVBDs) in clinic. However, most of these materials show a very low degradability due to a sintering process in their production. In this study, we synthesized a novel type of granules-biomimetically precipitated nanocrystalline calcium phosphate (BpNcCaP) by developing our previous biomimetic protocol. We evaluated the cytotoxicity of BpNcCaP by assessing the viability of L929 mouse fibroblasts using a 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H tetrazolium bromide (MTT) assay. To characterize the physicochemical properties of the novel BpNcCaP granules, we first compared the morphology and composition of BpNcCaP with those of Bio-Oss ® using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDS). We further compared the surface area, pore size distribution, hydrophilicity behavior, and hardness of BpNcCaP with those of Bio-Oss ® granules using specific surface area, contact angle, and Vickers hardness as parameters, respectively. BpNcCaP showed no obvious cytotoxicity. In-vitro characterization data showed that BpNcCaP and Bio-Oss ® granules were both comprised of nanocrystalline hydroxyapatite (HAp). The Ca/P ratios of BpNcCaP and Bio-Oss ® calculated from the EDS results were 1.34 and 1.66, respectively. Hence, BpNcCaP and Bio-Oss ® were Ca-deficient HAp. Compared with Bio-Oss ® , synthetic BpNcCaP had better hydrophilicity, higher specific surface area, lower crystallinity, and hardness. These data suggested a good performance of BpNcCaP granules in clinical applications.