Traditional antimicrobial therapies always rely on antibiotics, which have led to the overuse of antibiotics and caused the emergence of multidrug-resistant (MDR) bacteria in recent years. In this study, an efficient and broad-spectrum antimicrobial system based on chitosan (CS)-encapsulated multifunctional metal-organic nanoparticles (Fe-TCPP@CS NPs) was constructed to integrate the electrostatic targeting property and photodynamic and photothermal antimicrobial therapies. Tetrakis (4-carboxyphenyl) porphyrin (TCPP) coordinated with Fe3O clusters to form nanoparticles, Fe3O clusters enabled low-temperature photothermal therapy as well as avoiding the porphyrins self-aggregation to ensure the singlet oxygen yield under irradiation, and CS as the outer layer covered on Fe-TCPP nanoparticles could improve the dispersibility in aqueous solution and enhance the electrostatic binding with bacterial cell membranes to improve the antibacterial activities. After simple synthesis, we successfully obtained ideal and biocompatible multifunctional nanoparticles and verified their antimicrobial properties. Under light irradiation, Fe-TCPP@CS NPs could produce enough ROS and heat to kill S. aureus, E. coli and methicillin-resistant S. aureus with a synergistic effect. Therefore, Fe-TCPP@CS NPs would be an efficient and broad-spectrum antimicrobial agent, providing a novel approach to bacterial infection therapy.