As the increasing problem of bacterial resistance has become the threaten to human health and environmental protection, the explorations of efficient and environmental-friendly antimicrobial agents are highly desired. Recently, vacancy engineering is regarded as the quite novel strategy to regulate the electronic structure of semiconductor Nanomaterials (NMs), largely improving their photocatalytic performance in rapid and safe sterilization. In this study, molybdenumsulfide(MoS2) NMs with different concentrations of sulfur vacancies (Vs) were synthesized through annealed at different temperature (i.e., 150 °C, 250 °C and 350 °C), providing the platform for studying the efficient bacterial inactivation of defective MoS2 NMs under the near-infrared light irradiation. The optimum photothermal conversion efficiency could be achieved with the appropriate concentration of Vs, through improving the light adsorption and preventing the recombination of photogenerated e−/h+ pairs. In addition, MoS2 NMs with the abundant Vs exhibited hyperthermia and strong binding ability to bacteria, leading to the severe damage to cell wall integrity, energy supply and antioxidant system. Collectively, these results focused on the relationship between optimum antibacterial efficiency and appropriate concentrations of Vs, providing new insights into the designation of photocatalysts with highly efficient sterilization.