Antibiotics are widely used for treatment of bacterial infections, and their overuse has contributed to microbial resistance. Currently, an alternative antibiotic-free therapy for inactivating bacteria is of great interest. Black phosphorus (BP), a biocompatible and nontoxic rising-star two-dimensional layered material, has gained remarkable interest in many bioapplications including biosensing, cancer therapy, drug delivery, and also antibacterial treatment. However, BP nanosheets suffer from instability in ambient environments due to rapid oxidation and degradation. To address this issue, BP nanosheets were modified with quaternized chitosan (QCS) by electrostatic adsorption to prepare a BP-QCS composite for photothermal/pharmaco treatment of bacterial infection. The BP-QCS has obviously enhanced solubility and chemical stability in aqueous suspensions. We have demonstrated that under near-infrared (NIR) irradiation, the BP-QCS can synergistically inactivate more than 95% methicillin-resistant (. ) (MRSA) and within 10 min with a dose of only 75 μg/mL in vitro. Meanwhile, the BP-QCS composite under NIR can synergistically inactivate 98% in vivo Furthermore, the BP-QCS suspensions at effective antibacterial concentrations have negligible cytotoxicity and in vivo toxicity.