In this study, we evaluated the cellular behaviors of human bone marrow stromal cells(hBMSCs) on the surface of apatite pre-coated poly(ε-caprolactone)-organosiloxane nano-hybrid material(SiOPCL) and assessed the osteoconductivity of SiOPCL in the diaphyses of the rabbit tibiae. Polycaprolactone(PCL), which is backbone of its organic phase, was evaluated to confirm the advantages of a structural modification of SiOPCL. The attachment and proliferation of hBMSCs on both PCL and apatite pre-coated SiOPCL(SiOPCL/HAp) was comparable to those observed on tissue culture plates(TCPs). The alkaline phosphatase activity of hBMSCs on both PCL and SiOPCL/HAp was significantly higher on day 21 compared with those on the TCPs. There was newly formed bone, together with numerous osteoblasts, that was observed along the entire surface of the SiOPCL in the medullary canal of the rabbit tibiae with in vivo testing. There was no evidence of any adverse responses, such as inflammation or foreign body reactions, around the SiOPCL. However, we observed severe inflammatory reactions and foreign body responses, which was evidence of its degradation and resorption, without evidence of new bone formation after the implantation of PCL. These results demonstrated that SiOPCL had compatible hBMSCs responses and excellent osteoconductivity in vivo.