The rapid repair of bone defects remains a significant clinical challenge to this day. To address this issue, a 3D-printed biphasic calcium phosphate (BCP) scaffold consisting of 40 wt % hydroxyapatite (HA) and 60 wt % β-tricalcium phosphate (β-TCP) was created. Silicon and zinc were incorporated into HA and β-TCP, respectively, to enhance the angiogenic and osteogenic properties of the BCP scaffold. The physicochemical properties, in vitro cell responses, and bone defect repair efficacy of the modified BCP scaffold were comprehensively investigated. Results showed that the fabricated scaffold possessed a 3D interconnected pore structure. Zinc doping enhanced the sintering of the BCP scaffold, increased its density and strength, but decreased its degradation rate. Conversely, silicon doping had the opposite effect. The modified scaffold was capable of a gradual release of zinc/silicon ions, which promoted the proliferation and differentiation of cells. Specifically, the scaffold doped with zinc significantly promoted the osteogenic differentiation of stem cells. Moreover, co-doping with silicon and zinc synergistically promoted in vitro angiogenesis, with BCP-3 (doped with 2.5 mol % zinc and 4 mol % silicon) exhibiting the best pro-angiogenic activity. BCP-3 significantly induced regeneration of blood vessels and bone tissue in vivo, indicating its potential to accelerate the process of bone defect repair.