The increasing prevalence of multidrug-resistant (MDR) bacteria primarily due to the emergence of drug-resistant biofilms that have rendered current antimicrobial agents ineffective poses a significant concern in public health. Therefore, innovative antimicrobial agents need to be urgently developed. This study aimed to design a photodynamic antimicrobial nanocomposite (Ce6/HSF) based on chitosan quaternary ammonium salt (HTCC)-functionalized silk fibroin (SF) loaded with chlorin e6 (Ce6) for eliminating drug-resistant biofilms and bacteria. The prepared Ce6/HSF had low toxicity, good biocompatibility, and excellent ability to generate single-linear-state oxygen. In addition, Ce6/HSF can enter multidrug-resistant bacteria by electrostatic adsorption due to its small size and cationic nature. Furthermore, it effectively promoted wound healing in mice infected with MDR Staphylococcus aureus.