Building a novel and efficient photothermal antibacterial nanoplatform is a promising strategy for precise bacterial elimination. Herein, a nanocomposite NiO NPs@AuNPs@Van (NAV) for selective MRSA removal was constructed by electrostatic self-assembly of highly photothermal magnetic NiO NPs and vancomycin (Van)-modified gold nanoparticles (AuNPs). In the presence of MRSA and under NIR irradiation, Van-mediated AuNPs can self-aggregate on MRSA surface, generating photothermal effect in situ and killing 99.6% MRSA in conjunction with magnetic NiO NPs. Additionally, the photothermal efficiency can be improved by magnetic enrichment due to the excellent magnetism of NAV, thereby enhancing the bactericidal effect at a lower experimental dose. In vitro antibacterial experiments and full-thickness skin wound healing test demonstrated that this combination therapy could effectively accelerate wound healing in MRSA-infected mice, increase collagen coverage, reduce IL-6 and TNF-α content, and upregulate VEGF expression. Biological safety experiments confirmed that NAV has good biocompatibility in vivo and in vitro. Overall, this work reveals a new type of nanocomposite with enhanced photothermal antibacterial activity as a potential nano-antibacterial agent for treating bacteria-infected wounds.