Biologically, MoS₂-based nanostructures have been intensely applied for the photothermal therapy of cancer, but rarely for antibacterial uses. In this contribution, a multifunctional chitosan (CS) functionalized magnetic MoS₂ (abbreviated to CFM) was constructed to nonspecifically combat bacterial infection by integrating bacterial conjugation and enrichment, and NIR-triggered photothermal sterilization. Owing to the abundant introduced amino groups, the CFM complex offers a significantly enhanced conjugation efficiency without obvious specificity towards both Gram-positive and -negative bacteria compared to amino-free magnetic MoS₂. The magnetic properties of CFM obtained from iron oxide facilitate the enrichment of a CFM–bacteria conjugate, improving the photothermal efficiency of CFM as a photothermal antibacterial agent. Specifically, after being trapped together with bacteria cells, CFM shows an enhanced in vitro photothermal sterilization ability. In vivo S. aureus-induced abscess treatment studies show faster healing when CFM is used as subcutaneous nano-localized heating sources with the assistance of an external magnet to concentrate the CFM–bacteria conjugate. This work establishes an innovative solution and a novel antimicrobial agent for combating bacterial infections without the use of antibiotics, which may open a new area of application and research for MoS₂-based nanostructures.