The problem of antimicrobial resistance (AMR) caused by the abuse of antibiotics is becoming serious. The development of antibacterial materials with synergistic efficiency and treatment of deep tissue/organ infections is imminent. Herein, synergistic antibacterial nanoparticles (MPH NPs) are prepared by loading antibacterial peptide polymyxin B (PMB) on Fe‐based MOF (MIL‐100) with hyaluronic acid (HA) modification. MPH NPs exerts antibacterial effects by chemodynamic therapy (CDT) and the release of PMB. MPH NPs have broad‐spectrum antibacterial properties on Gram‐negative bacteria (E. coli, 100%), Gram‐positive bacteria (S. aureus, 98.5 %), and MRSA (98.4%). Importantly, MPH NPs not only promote the healing of infected wounds but also target lungs to accomplish organ infection therapy. Therefore, this study provides a new strategy for designing a synergetic anti‐AMR bacteria system and the function for deep tissue/organ infection therapy in the future.