Large-sized bone defect repair is a challenging task in orthopedic surgery. Porous scaffolds with controlled release of growth factors have been investigated for many years. In this study, a hydroxyapatite composite scaffold was prepared by 3D printing at low temperature and coating with layer-by-layer (LBL) assembly. Bone morphogenic protein-2 (BMP-2) and vascular endothelial growth factors (VEGF) were loaded into the composite scaffolds. The release of dual growth factors was analyzed in vitro. The cell growth and osteogenic differentiation were assessed by culturing MC3T3-E1 cells onto the scaffolds. In an established rabbit model of critical-sized calvarial defect (15 mm in diameter), the osteogenic and angiogenic properties after implantation of scaffolds were evaluated by micro-computed tomography (micro-CT) and stained sections. Our results showed that the scaffolds possessed well-designed porous structure and could release two growth factors in a sustained way. The micro-CT analysis showed that the scaffolds with BMP-2/VEGF could accelerate new bone formation. Findings of immunochemical staining of collagen type I and lectin indicated that better osteogenic and angiogenic properties induced by BMP-2 and VEGF. These results suggested that the novel composite scaffolds combined with BMP-2/VEGF had both osteogenic and angiogenic abilities which could enhance new bone formation with good quality. Thus, the combination of 3D printed scaffolds loaded with BMP-2/VEGF might provide a potential solution for bone repair and regeneration in clinical applications.