We have developed a biocompatible antibacterial system based on polyethylene glycol functionalized molybdenum disulfide nanoflowers (PEG-MoS2 NFs). The PEG-MoS2 NFs have high near-infrared (NIR) absorption and peroxidase-like activity, which can efficiently catalyze decomposition of low concentration of H2O2 to generate hydroxyl radicals (center dot OH). The conversion of H2O2 into center dot OH can avoid the toxicity of high concentration of H2O2 and the center dot OH has higher antibacterial activity, making resistant bacteria more vulnerable and wounds more easily cured. The PEG-MoS2 NFs combine the catalysis with MR photothermal effect, providing a rapid and effective killing outcome in vitro for Gram-negative ampicillin resistant Escherichia coli (Amp(r) E. coli) and Gram-positive endospore-forming Bacillus subtilis (B. subtilis) as compared to catalytic treatment or photothermal therapy (PTT) alone. Wound healing results indicate that the synergy antibacterial system could be conveniently used for wound disinfection in vivo. Interestingly, glutathione (GSH) oxidation can be accelerated due to the 808 mu irradiation induced hyperthermia at the presence of PEG-MoS2 NFs proved by X-ray near-edge absorption spectra and X-ray spectroscopy. The accelerated GSH oxidation can result in bacterial death more easily. A mechanism based on center dot OH-enhanced PTT is proposed to explain the antibacterial process.