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In this study, we developed a poly(β-amino ester) (PBAE) hydrogel for the double release of vancomycin (VAN) and total flavonoids of Rhizoma Drynariae (TFRD). VAN was covalently bonded to PBAE polymer chains and was released to enhance the antimicrobial effect first. TFRD chitosan (CS) microspheres were physically dispersed in the scaffold, TFRD was released from the microspheres, and osteogenesis was induced subsequently. The scaffold had good porosity (90.12 ± 3.27%), and the cumulative release rate of the two drugs in PBS (pH 7.4) solution exceeded 80%. In vitro antimicrobial assays demonstrated the antibacterial properties of the scaffold against Staphylococcus aureus(S. aureus) and Escherichia coli(E. coli). Besides these, cell viability assays indicated that the scaffold had good biocompatibility. Moreover, alkaline phosphatase and matrix mineralization were expressed more than in the control group. Overall, cell experiments confirmed that the scaffolds have enhanced osteogenic differentiation capabilities. In conclusion, the dual-drug-loaded scaffold with antibacterial and bone regeneration effects is promising in the field of bone repair.