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Carbonate apatite (CO 3 Ap)-granules bone substitute exhibits excellent osteoconductivity and replaced by a new bone based on bone remodeling process. However, no improvement has been made so far with respect to the drawbacks of granules; i.e., intraoperative scatter and postoperative migration. The aim of this study was to evaluate the feasibility of fabricating a CO 3 Ap-granules sponge to overcome these drawbacks. The CO 3 Ap granules sponge was successfully fabricated by mixing 300–600 µm CO 3 Ap granules with 3 % atelocollagen, followed by lyophilization at − 70 °C for 24 h and a dehydrothermal treatment at 150 °C for 24 h. The CO 3 Ap-granules sponge and CO 3 Ap-granules were implanted into rat calvarial bone defects for 2 and 4 weeks. No significant intraoperative scatter and postoperative migration were evident when the bone defects were reconstructed with the CO 3 Ap-granules sponge, whereas significant both intraoperative scatter and postoperative migration were observed when the bone defect was reconstructed with CO 3 Ap granules. Although less osteogenesis was anticipated for the CO 3 Ap-granules sponge due to the coverage of CO 3 Ap-granules surface with atelocollagen, no significant differences were observed in bone formation between the CO 3 Ap-granules sponge and CO 3 Ap-granules cases because the 3 % atelocollagen and lyophilization kept the CO 3 Ap granules surface only partially covered. Consequently, the CO 3 Ap-granules sponge and CO 3 Ap-granules exhibited similar bone formation at both 2 and 4 weeks after surgery. Thus, the CO 3 Ap-granules sponge improved the handling performance and retention ability at the bone defects without scarifying the osteogenesis of CO 3 Ap-granules. [ABSTRACT FROM AUTHOR]