Nanozymes with good biocompatibility are novel antibacterial agents because they mimic the structure and properties of enzymes and destroy bacterial structures by generating reactive oxygen species in large quantities. Herein, we synthesized a Cu single-atom nanozyme (Cu-N-C) with intrinsic peroxidase- and oxidase-like activities. Cu-N-C can generate ·OH and O2·- during oxidase-catalyzed reactions, which have good antibacterial effects. Meanwhile, the antimicrobial performance can be further enhanced by light emitting diode light incubation due to photocatalysis. Lethal disruption of the membrane structure was confirmed by biofilm staining and scanning electron microscopy analysis. Notably, the antibacterial effect of Cu-N-C (MIC = 16 μg/mL) was significantly better than that of vancomycin (MIC = 1500 μg/mL), a commonly used drug for methicillin-resistant Staphylococcus aureus, and Cu-N-C outperformed the positive control cephalexin and gentamicin in terms of resistance development (27.3% less production of drug-resistant bacteria). Good biocompatibility was also verified using the MTT method, hemolysis analysis, and routine blood measurements in mice. The results of this work suggest that Cu-N-C has great potential for clinical applications as an efficient metal antimicrobial agent.