Oral and maxillofacial bone defect repair in patients remains challenging in clinical treatment due to the different morphologies of bone defects. An injectable hydrogel of microspheres with sustained bone morphogenetic protein 9 (BMP9) expression for oral and maxillofacial bone defect repair has been developed. This study is bioinspired by the substantial osteogenesis property of recombinant adenoviruses expressing bone morphogenetic protein 9 (Ad-BMP9) and minimally invasive treatment by injection. A novel scaffold encompassing bone mesenchymal stem cells (BMSCs) transfected with Ad-BMP9 was produced and cocultured on a superficial surface of monodisperse photocrosslinked methacrylate gelatin hydrogel microspheres (GelMA/MS, produced with microfluidic technology). The biological tests including live/dead cell staining, phalloidin staining, cell counting kit-8 (CCK-8) assay, alkaline phosphatase (ALP) activity and staining, alizarin red S staining, and quantitative real-time polymerase chain reaction (RT-qPCR), revealed that the hydrogel microspheres exhibited good biocompatibility and remarkably promoted the osteogenic differentiation of BMSCs in vitro. In addition, a small needle was injected the innovative scaffold beneath the nude mice’s skin. The micro-CT and histological staining assay results demonstrated that the new implant, with high blood vessel formation markers (CD31-positive cells) expression over four and eight weeks, achieved significant vascularized bone-like tissue formation. Consequently, the injectable hydrogel microspheres, cocultured with BMSC transfected with Ad-BMP9, enhanced vascularized bone regeneration, therefore representing a facile and promising technique for the minimally invasive treatment of oral and maxillofacial bone defects.