Critical-sized bone defects repair remains a major clinical challenge that requires scaffolds with angiogenesis and osteogenesis potential. Herein, we synthesized zinc (Zn) -doped and zinc/magnesium (Zn/Mg) co-doped hydroxyapatite (HA) via hydrothermal method, and then mixed it with polycaprolactone (PCL) as ink to fabricate composite scaffolds through 3D printing. We explored the potential of composite scaffolds in promoting angiogenesis and osteogenesis. In vitro experiments demonstrated that Zn/Mg co-doped composite scaffolds can promote angiogenesis. In addition, Zn/Mg co-doped scaffolds could promote osteogenesis and was superior to Zn doped composite scaffolds. Furthermore, in vivo studies using a rat femoral defect model confirmed the Zn/Mg co-doped scaffolds repaired bone defects. Thus, the Zn/Mg co-doped composite scaffolds developed in this study were effective for angiogenesis and bone defect repair, which provide an excellent solution for the design and development of clinical materials.