Safe and effective antimicrobial treatment strategies are urgently required for the prevention and control of infectious diseases. While silver-based nanoparticles (AgNPs) are currently acknowledged as the most potent metal-based antibacterial agents, their potential cytotoxicity poses a significant barrier to further clinical applications. Herein, we synthesized carbonaceous coated silver nanocore (Ag@C) core-shell nanoparticles and investigated their material properties, biocompatibility, and antibacterial efficacy. The produced Ag@C exhibited a uniform core-shell structure with an overall diameter of 256.40 nm, a shell thickness of 92.20 nm, and a silver core diameter of 67.45 nm. Under irradiation with 808 nm near-infrared (NIR) irradiation, Ag@C demonstrated excellent photothermal conversion efficiency. The results from apoptosis detection via flow cytometry, CCK-8 cytotoxicity assays, and live/dead cell staining using Calcein-AM/PI, collectively indicated that Ag@C displayed no significant cytotoxicity. Hemolysis tests further confirmed the good biocompatibility of Ag@C. Quantitative analysis through plate counting assays revealed that Methicillin-resistant Staphylococcus aureus (MRSA) co-cultured with Ag@C were significantly eradicated by NIR irradiation; this finding was corroborated by bacterial live/dead staining observed under confocal laser scanning microscope (CLSM). Our results indicate that Ag@C combined with photothermal therapy (PTT) exhibits substantial antibacterial effects in vitro while maintaining high biosafety standards, suggesting promising prospects for clinical application.