The purpose of this study was to evaluate the osteogenic capacity of water extract of danshen. We have established in rat critical-sized calvarial defect model using the combination with collagen scaffold and danshen hydrophilic extract. All rats were extinguished at 8 weeks after bone graft surgery, and the bone regeneration ability of bone grafting sides was evaluated by plain radiography and micro-CT. These results revealed water extract of danshen had the potential to promote osteogenesis especially continuous oral administration with local treatment compared to one-shot local treatment. This compound may provide a new alternative agent for growth factors to promote bone healing and bone regeneration. In conclusion, these results suggest that danshen hydrophilic extract have the potential to promote osteogenesis in bone defects. Further studies about fusion technology with salvianolic acid B, peptides, growth factors, and scaffolds using of the combination of tissue engineering, cell engineering and mechanical engineering are needed.