We have established a processing method to fabricate three-dimensional porous carbonate apatite (CO3Ap) with interconnected porous structure and improved mechanical strength. Briefly, porous CO3Ap materials were produced via phosphorization of porous calcite precursor in hydrothermal condition. In order to make porous calcite precursor, negative replication of modified polyurethane foam template was conducted. In this study, an in vivo behavior of that porous CO3Ap was evaluated. The interconnected porous CO3Ap material was implanted in the tibia of Japanese male rabbits and removed after a period of 6 months. Micro-computed tomography (μ-CT) scanner and histological analysis were used to characterize the bone formation response of the porous CO3Ap. The results suggest that porous CO3Ap with enhanced mechanical strength was not only osteoconductive but also bioresorbable therefore it could be used as bone substitute material.