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To develop a safe, efficient, water-soluble, and targeted antibacterial substance for medical applications, we synthesized carbon dots using citric acid and urea as precursors by a solvothermal method. We then coupled the carbon dots and lysozyme by using a simple 1-ethyl-3-(3'-dimethylaminopropyl) carbodiimide-N–hydroxysuccinimide (EDC-NHS) coupling method. After coupling, the carbon dots exhibited improved water dispersibility with particle sizes ranging from 12 to 20 nm. Notably, the highest carbon dot concentration associated with cytotoxicity increased from 2.5 to 5 mg/mL when coupled with lysozyme, implying that coupling could enhance the biocompatibility of carbon nanodots. Furthermore, coupled carbon dots extended the effective inhibition time against Streptococcus mutans from 12 to 36 h, compared to carbon dots alone. The improved biocompatibility and prolonged effective antibacterial duration highlight the potential of lysozyme-coupled carbon dots as a safe, efficient, and water-soluble antibacterial agent for a variety of oral healthcare and medical applications.