Photothermal therapy is an ideal non-invasive treatment for bacterial infections. However, if photothermal agents are unable to target bacteria, they can also cause thermal damage to healthy tissue. This study describes the fabrication of a Ti3C2Tx MXene-based photothermal nanobactericide (denoted as MPP) that targets bacteria by modifying MXene nanosheets with polydopamine and the bacterial recognition peptide CAEKA. The polydopamine layer blunts the sharp edges of MXene nanosheets, preventing their damage to normal tissue cells. Furthermore, as a constituent of peptidoglycan, CAEKA can recognize and penetrate the bacterial cell membrane based on similar compatibility. The obtained MPP exhibits superior antibacterial activity and high cytocompatibility compared to the pristine MXene nanosheets. In vivo studies showed that MPP colloidal solution under 808 nm NIR light can effectively treat a subcutaneous abscess caused by multi-drug resistant bacterial infection without adverse effects.