Three-dimensional interconnected porous carbonate apatite (3D-CO3Ap) bone grafts facilitate rapid bone replacement because of their structure, which supports cellular infiltration. Existing 3D-CO3Ap grafts have demonstrated limited mechanical strength, with a maximum compressive strength of 3 MPa. By fusing polymer-bound CaCO3 granules, followed by the debinding and compositional transformation of the granules via a dissolution–precipitation reaction, we successfully fabricated 3D-CO3Ap grafts that exhibited remarkably enhanced compressive strengths, which were recorded at 14.9 ± 3.7 MPa. The use of spherical granules, which provide more uniform and effective intergranular contacts than cylindrical granules, was key to achieving higher mechanical strength and superior bone formation. 3D-CO3Ap developed with spherical granules not only exhibited higher compressive strength, but also enhanced new bone formation compared with those fabricated with cylindrical granules. This study underscores the significance of porous microstructure design in 3D-CO3Ap, highlighting its critical role in optimizing both mechanical properties and bone regeneration capabilities.