Developing efficient therapeutic strategies for combating bacterial infection remains a challenge owing to the indiscriminate utilization of antibiotics and the prevalence of multidrug-resistant (MDR) bacteria. Herein, highly graphitic-N-doped graphene quantum dots (N-GQDs) with efficient NIR-II photothermal conversion properties were synthesized for the first time for photothermal antibacterial therapy. The obtained N-GQDs exhibited strong NIR absorption ranging from 700 to 1200 nm, achieving high photothermal conversion efficiency of 77.8% and 50.4% at 808 and 1064 nm, respectively. Outstanding antibacterial and antibiofilm activities against MDR bacteria (methicillin-resistant Staphylococcus aureus, MRSA) were achieved by the N-GQDs in the presence of an 808 or 1064 nm laser. In vivo investigations verified that the generation of hyperthermia by N-GQDs plus a NIR-II laser can combat MDR bacterial infections and thus significantly accelerate wound healing. Our work provides a novel carbon-based nanomaterial as a photothermal antibacterial agent for efficiently avoiding bacterial resistance and fighting MDR bacterial infections.