Injectable calcium phosphate cement (CPC) offers significant benefits for the minimally invasive repair of irregular bone defects. However, the main limitations of CPC, including its deficiency in osteogenic properties and insufficient large porosity, require further investigation and resolution. In this study, alginate-chitosan-alginate (ACA) microcapsules were used to encapsulate and deliver rat bone mesenchymal stem cells (rBMSCs) into CPC paste, while a porous CPC scaffold was established to support cell growth. Our results demonstrated that the ACA cell microcapsules effectively protect the cells and facilitate their transport into the CPC paste, thereby enhancing cell viability post-implantation. Additionally, the ACA + CPC extracts were found to stimulate osteogenic differentiation of rBMSCs. Furthermore, results from a rat cranial parietal bone defect model showed that ACA microcapsules containing exogenous rBMSCs initially improved thein situosteogenic potential of CPC within bone defects, providing multiple sites for bone growth. Over time, the osteogenic potential of the exogenous cells diminishes, yet the pores created by the microcapsules persist in supporting ongoing bone formation by recruiting endogenous cells to the osteogenic sites. In conclusion, the utilization of ACA loaded stem cell microcapsules satisfactorily facilitate osteogenesis and degradation of CPC, making it a promising scaffold for bone defect transplantation.