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There is an urgent need for materials that can efficiently generate reactive oxygen species (ROS) and be used in photodynamic therapy (PDT) as two-photon imaging contrast probes. In this study, graphene quantum dots (GQDs) were subjected to amino group functionalization and nitrogen doping (amino-N-GQDs) via annealing and hydrothermal ammonia autoclave treatments. The synthesized dots could serve as a photosensitizer in PDT and generate more ROS than conventional GQDs under 60-s low-energy (fixed output power: 0.07 W·cm⁻²) excitation exerted by a 670-nm continuous-wave laser. The generated ROS were used to completely eliminate a multidrug-resistant strain of methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), a Gram-positive bacterium. Compared with conventional GQDs, the amino-N-GQDs had superior optical properties, including stronger absorption, higher quantum yield (0.34), stronger luminescence, and high stability under exposure. The high photostability and intrinsic luminescence of amino-N-GQDs contribute to their suitability as contrast probes for use in biomedical imaging, in addition to their bacteria tracking and localization abilities. Herein, the dual-modality amino-N-GQDs in PDT easily eliminated multidrug-resistant bacteria, ultimately revealing their potential for use in future clinical applications.