A composite scaffold integrating biphasic calcium phosphate (BCP) with sodium alginate (SA) was engineered in this study to facilitate the repair of bone defects. Nacre-derived BCP with different ratios of hydroxyapatite (HAP) to β-tricalcium phosphate (β-TCP)—H5 (50:50) and H3 (30:70)—were combined with SA, cross-linked with calcium ions, and freeze-dried to fabricate three types of scaffolds: SN (SA alone), SH3, and SH5. Characterization revealed high crystallinity, porosity (65%–80%), and a pore size of approximately 100 μm. In vitro, SH5 scaffolds promoted MC3T3-E1 cell adhesion, proliferation, and differentiation, significantly enhancing osteogenesis-related gene expression (COL-1, RUNX-2, ALP, OPN) and alkaline phosphatase activity, while also supporting HUVEC migration and tube formation. In vivo, SH5 scaffolds exhibited superior bone regeneration, mineralization, collagen deposition, and integration with host tissue in a rat cranial defect model, accompanied by strong osteocalcin, osteopontin and osteoprotegerin expression. Experimental findings revealed that the SH5 BCP/SA scaffold possesses outstanding osteoinductive and angiogenic properties, thereby reinforcing its potential to be applied as bone defect repair substitutes.