An effective local drug delivery system remains an urgently needed product for the treatment of chronic osteomyelitis in the clinic. In this study, we developed an antibacterial functionalization bone graft by immobilizing levofloxacin hydrochloride-loaded mesoporous silica microspheres (LFH @ MSNs) on the surface of a nanohydroxyapatite/polyurethane (n-HA/PU) bioactive composite scaffold. Through pretreatment of the n-HA/PU scaffold by chitosan solution and subsequent crosslinking by vanillin, LFH @ MSNs were uniformly and stably immobilized on the scaffold surface. The results of drug release experiments showed that the release of LFH from LFH @ MSN-modified n-HA/PU scaffolds (LFH @ MSN/n HA/PU) lasted up to 42d. The antibacterial assays indicated that LFH @ MSN/n-HA/PU offers satisfactory antibacterial activity against both gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria. The biosafety assays demonstrated that the LFH @ MSN/n-HA/PU scaffold could satisfy the requirements of the biosafety standards. The constructed LFH @ MSN/n-HA/PU porous scaffolds with an antibacterial surface and favorable biosafety are deemed a promising candidate for infectious bone defect repair.