This study aimed to elucidate the local effect and micro-computed tomographic (μ-CT) assessment following bone implantation of an innovative bioceramic (α-calcium sulfate hemihydrate; α-CSH) on femur lateral condyle cortical bone of rabbit models. The innovative α-CSH bioceramic was synthesized through a green processing technology (microwave irradiation treatment). The bilateral implantation model was performed among 24 New Zealand White rabbits which were divided into three groups based on the type of filling materials: α-CSH, control, and blank. Treatments were performed in defects with 6 mm diameter and 7 mm depth and observed after 2, 4, 8, and 12 weeks. Material reaction and bone formation after implantation were evaluated radiographically and histopathologically. The μ-CT analysis results showed that the degradation of α-CSH and control material was similar at 4 and 8 weeks. The bone volume in the defects indicated the α-CSH increased most in 8 weeks. In histopathological evaluation, the α-CSH group was repaired with lamellar bone and well-grown bone marrow infiltration similar to the control material. Moreover, the α-CSH revealed a faster degradation rate and better healing progress than the control material under the same conditions. Therefore, the α-CSH was confirmed to be useful in promoting osteoconduction and in controlling the resorption rate in bone defects. Further, the innovative α-CSH could be considered as a promising bone substitute for utilization in bone reconstructive therapy in dental and orthopedic fields.