In recent years, borosilicate bioactive glass (BBG) is widely studied due to its osteoinductive activities. However, the ions accumulated in the extracts can induce cytotoxicity and hemolysis when evaluating the biological properties of the degradable materials using the extracts of the materials. In this paper, the BBGs were prepared at different ratios of B2O3 (0B, 1.5B, and 3.0B samples), and bone cements were fabricated by mixing the BBGs with 30% (in mass fraction) citric acid. The cytotoxic and osteogenic effects of the bone cements extracts were evaluated using human bone marrow mesenchymal stem cells (hBMSCs), and the bone healing effects of the bone cements were evaluated using a rat femoral defect model, respectively. The results show that the extracts of bone cement formed at a greatest ratio of B2O3 in the bioactive glass can induce a maximum inhibitive effect on the proliferation and osteogenesis of hBMSCs in vitro. However, the degradation and bone healing effect of the bone cement increase directly with the ratio of B2O3 in BBG upon transplantation. Also, there is a huge discrepancy with the in vivo and in vitro evaluation systems for the biodegradable biomaterials. Understanding the mechanisms of the different biological effects of BBG in vitro and in vivo will provide some guidance for the design of a more effective borate-containing bioactive materials and the construction of a better evaluation system for bioactive materials in vitro, thus facilitating the clinical applications of BBG.