The fabrication of bone tissue engineering scaffolds with high osteogenic ability and favorable mechanical properties is of huge interest. In this study, a silk fibroin (SF) solution of 30 wt% was extracted from cocoons and combined with mesoporous bioactive glass (MBG) to fabricate MBG/SF composite scaffolds by 3D printing. The porosity, compressive strength, degradation and apatite forming ability were evaluated. The results illustrated that MBG/SF scaffolds had superior compressive strength (ca. 20 MPa) and good biocompatibility, and stimulated bone formation ability compared to mesoporous bioactive glass/polycaprolactone (MBG/PCL) scaffolds. We subcutaneously transplanted hBMSCs-loaded MBG/SF and MBG/PCL scaffolds into the back of nude mice to evaluate heterotopic bone formation assay in vivo, and the results revealed that the gene expression levels of common osteogenic biomarkers on MBG/SF scaffolds were significantly better than MBG/PCL scaffolds. These results showed that 3D-printed MBG/SF composite scaffolds are great promising for bone tissue engineering.