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 (·OH). The conversion of H₂O₂ into ·OH can avoid the toxicity of high concentration of H₂O₂ and the ·OH has higher antibacterial activity, making resistant bacteria more vulnerable and wounds more easily cured. The PEG-MoS₂ NFs combine the catalysis with NIR 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 nm 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 ·OH-enhanced PTT is proposed to explain the antibacterial process.