The development of biomaterials capable of accelerating bone wound repair is a critical focus in bone tissue engineering. This study aims to evaluate the osteointegration and bone regeneration potential of a novel multilayer gelatin-supported Bone Morphogenetic Protein 9 (BMP-9) coated nano-calcium-deficient hydroxyapatite/poly-amino acid (n-CDHA/PAA) composite biomaterials, focusing on the material-bone interface, and putting forward a new direction for the research on the interface between the coating material and bone. The BMP-9 recombinant adenovirus (Adenovirus (Ad)-BMP-9/Bone Marrow Mesenchymal Stem Cells (BMSc)) was produced by transfecting BMSc and supported using gelatin (Ad-BMP-9/BMSc/Gelatin (GT). Multilayer Ad-BMP-9/BMSc/GT coated nano-calcium deficient hydroxyapatite/polyamino acid (n-CDHA/PAA) composite biomaterials were then prepared and co-cultured with MG63 cells for 10 days, with biocompatibility assessed through microscopy, Cell Counting Kit-8 (CCK-8), and alkaline phosphatase (ALP) assays. Subsequently, multilayer Ad-BMP-9/BMSc/GT coated n-CDHA/PAA composite biomaterial screws were fabricated, and the adhesion of the coating to the substrate was observed using scanning electron microscopy (SEM). In vivo studies were conducted using a New Zealand White rabbit intercondylar femoral fracture model. The experimental group was fixed with screws featuring multilayer Ad-BMP-9/BMSc/GT coatings, while the control groups used medical metal screws and n-CDHA/PAA composite biomaterial screws. Fracture healing was monitored at 1, 4, 12, and 24 weeks, respectively, using X-ray observation, Micro-CT imaging, and SEM. Integration at the material-bone interface and the condition of neo-tissue were assessed through these imaging techniques. The Ad-BMP-9/GT coating significantly enhanced MG63 cell adhesion, proliferation, and differentiation, while increasing BMP-9 expression in vitro. In vivo studies using a rabbit femoral fracture model confirmed the biocompatibility and osteointegration potential of the multilayer Ad-BMP-9/BMSc/GT coated n-CDHA/PAA composite biomaterial screws. Compared to control groups (medical metal screws and n-CDHA/PAA composite biomaterial screws), this material demonstrated faster fracture healing, stronger osteointegration, and facilitated new bone tissue formation with increased calcium deposition at the material-bone interface. The multilayer GT-supported BMP-9 coated n-CDHA/PAA composite biomaterials have demonstrated favorable osteogenic cell interface performance, both in vitro and in vivo. This study provides a foundation for developing innovative bone repair materials, holding promise for significant advancements in clinical applications.