Even with advances in diverse antibiotics, bacterial infectious diseases with high mortality and morbidity still seriously endanger human health, which spurs the development of alternative antiseptic and therapeutic strategies for combatting bacteria. Antimicrobial photodynamic inactivation (aPDI) has emerged as an effective treatment protocol for different types of infection. Moreover, the risk from Gram-positive organisms cannot be overlooked. In the present work, fluoroborondipyrrole (BODIPY) was assembled with cationic and anionic carbon dots (CDs) to construct positively charged (termed p-BDP) and negatively charged (termed n-BDP) nanophotosensitizers. Compared with n-BDP, p-BDP showed a stronger photoinactivation activity against Staphylococcus aureus, and its minimal inhibitory concentration (MIC) was as low as 128 ng mL-1. In addition, p-BDP could act as a more efficacious wound dressing to accelerate the healing of S. aureus infections. This work opens up alternative thinking for the design of highly effective nanobactericides.