Objective To prepare a three-dimensional (3D) printing polylactic acid glycolic acid (PLGA) scaffold with bone morphogenetic protein-9 (BMP-9) and P-15 peptide hydrogel and evaluate its application in treating bone defects in rabbits. Methods 3D printing PLGA scaffolds were formed and scanned by electron microscopy. Their X-ray diffraction (XRD), in vitro degradation, and compressive strength were characterized. BMP-9 and P-15 hydrogels were prepared. Flow cytometry was used to detect apoptosis, and an electron microscope was used to evaluate cell adhesion to scaffolds. Alkaline phosphatase (ALP), type 1 collagen (Col-I), osteocalcin (OCN), runt-related transcription factor 2 (RUNX2), and osterix (SP7) were detected by western blotting. MicroCT was used to detect new bone formation, and bone tissue-related protein expressions were determined in the rabbit model with bone defects. Results The 3D printing scaffolds were cylindrical, and the inner diameter of the scaffolds was about 1 mm. The bread peak with wide distribution showed that the 3D printing only involved a physical change, which did not change the properties of the materials. The degradation rate of scaffolds was 9.38%, which met the requirements of properties of biological scaffolds. The water absorption of the support was about 9.09%, and the compressive strength was 15.83 N/mm2. In the coculture of bone marrow mesenchymal stem cells (BMSCs) with scaffolds, the 2% polypeptide hydrogel showed the most obvious activity in promoting the differentiation of BMSCs. Flow cytometry showed that the 0% and 2% groups did not cause obvious apoptosis compared with the control group. Scaffolds with 2% and 4% polypeptide promoted the expression of ALP, COL-1, OCN, RUNX2, and Sp7 in BMSCs. In vivo experiments showed that the expression of ALP, COL-1, OCN, RUNX2, and Sp7 protein in the 2% polypeptide scaffold group increased significantly compared with the model group. MicroCT detection demonstrated that the 2% polypeptide scaffold had good bone repair ability. Conclusion The PLGA scaffolds combined with BMP-9 and P-15 peptide hydrogels had good biological and mechanical properties and could repair bone defects in rabbits.