Cu-based nanomaterials have been developed to alleviate the problem of antibiotic resistance due to their superior properties and good biocompatibility. Defects in nanomaterials have a major role in improving photocatalytic performance. Herein, two CuS nanospheres with predominant V and V vacancy (abbreviated as CuS and CuS-T150, respectively) characterized by positron annihilation spectra are synthesized. The combination of experimental and theoretical calculation results demonstrates that CuS-T150 exhibits excellent antibacterial, achieving bactericidal rates of 99.9% against to Escherichia coli (E. coli) under 808 nm laser irradiation. Compared with CuS, the superior antimicrobial activity of CuS-T150 is mainly attributed to its stronger ability to adsorb oxygen molecules, more easily bind with surface of E. coli, and higher photothermal conversion efficiency (PTCE). This work provides a deeper understanding of nanomaterials with vacancy modulated the antibacterial efficiency by synergistic effect of photodynamic and photothermal therapy.