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Granular bone substitutes are commonly used in dental treatments owing to their adaptability to irregular bone defects. However, granule migration during and after implantation poses a significant challenge, impairing bone regeneration. This study addresses this issue by setting carbonate apatite (CAp) granules using crystal interlocking owing to the bassanite (calcium sulfate hemihydrate (CSH))-to-gypsum (calcium sulfate dihydrate (CSD)) transformation on the granule surface. CAp granules were mixed with CSH slurry (water/CSH ratio of 0.4) at varying CSH/CAp ratios of 0.33, 0.43, 0.54, 0.67, and 0.82. At all of these mixing ratios, needle-shaped CSD crystals formed on the CAp granule surface, and the CSD crystals interlocked with each other; consequently, CAp granules were set. As the CSH/CAp ratio increased from 0.33 to 0.82, the CSD crystal length increased from 6.58 to 6.79 μm, while the setting time decreased from 30.3 to 15.5 min. Although the porosity of the set CAp granules decreased with an increase in the CSH/CAp ratio, the set granules maintained intergranular spaces of 77.3 μm at a CSH/CAp ratio of 0.82 conducive to cellular infiltration. After immersion in saline for six days, the set CAp granules at a CSH/CAp ratio of 0.82 maintained their original shape, demonstrating enhanced stability compared to lower CSH/CAp ratios where partial or complete collapse occurred. The porosity and specific surface area increased to 59.9% and 3.66 m2/g, respectively, and the intergranular spaces increased to 176.4 μm. Therefore, mixing the CAp granules with CSH at a ratio of 0.82 may prevent granule migration during and after implantation. Moreover, the CSD component of the granules is likely to resorb more rapidly than the CAp component in vivo, promoting porosity in the set granules and facilitating efficient bone replacement.