Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) are the most common infectious bacteria in our daily life, and seriously affect human’s health. Because of the frequent and extensive use of antibiotics, the microbial strains forming drug resistance have become more and more difficult to deal with. Herein, we utilized bovine serum albumin (BSA) as the template to synthesize uniform copper sulfide (CuS) nanoparticles via a biomineralization method. The as-prepared BSA-CuS nanocomposites showed good biocompatibility and strong near-infrared absorbance performance and can be used as an efficient photothermal conversion agent for pathogenic bacteria ablation with a 980 nm laser at a low power density of 1.59 W/cm2. The cytotoxicity of BSA-CuS nanocomposite was investigated using skin fibroblast cells and displayed good biocompatibility. Furthermore, the antibacterial tests indicated that BSA-CuS nanocomposite showed no antibacterial activity without NIR irradiation. In contrast, they demonstrated satisfying killing bacterial ability in the presence of NIR irradiation. Interestingly, S. aureus and E. coli showed various antibacterial mechanisms, possibly because of the different architectures of bacterial walls. Considering the low cost, easy preparation, excellent biocompatibility and strong photothermal convention efficiency (24.68%), the BSA-CuS nanocomposites combined with NIR irradiation will shed bright light on the treatment of antibiotic-resistant pathogenic bacteria.