This study evaluated the possibility of clinical application using matrigel-based bioceramic/polymer scaffolds treated with bone morphogenetic protein, angiogenic factor, and mesenchymal stem cells (MSCs) for new bone formation. In the in vitro study, bone morphogenetic protein (BMP-2) and vascular endothelial growth factor (VEGF) containing matrigel, which is a basement membrane gel, was injected into HA/PCL scaffolds to estimate the release rates of growth factors. In the in vivo study, BMP-2, VEGF, and MSCs with matrigel-based scaffolds were implanted into rat femoral segmental defects, and new bone formation was evaluated at 4 and 8 weeks. In the results, the release rates of BMP-2 and VEGF explosively increased by day 5. For the in vivo study results, radiological evaluation revealed that the matrigel-based HA/PCL scaffolds with BMP-2 and VEGF grafted (M+B+V) and matrigel-based HA/PCL scaffolds with BMP-2, VEGF, and MSC grafted (MSC) groups showed increased bone volume and bone mineral density. Moreover, in the histological evaluation, large new bone formation was observed in the M+B+V group, and high cellularity in the scaffold was observed in the MSC group. In conclusion, grafted matrigel-based HA/PCL scaffolds with BMP-2, angiogenic factor, and MSCs increased new bone formation, and in clinical cases, it may be effective and useful to enhance healing of delayed fractures.