The invention discloses a fluorine-containing graphene quantum dot, a preparation method and application thereof as a photodynamic therapy photosensitizer, and belongs to the field of biomedical materials. The average thickness of the prepared fluorine-containing graphene quantum dot is 1.0-3.0 nanometers, the size is 2.0-3.0 nanometers, the fluorine content is 1%-2%, the oxygen content is 20%-30%, and the carbon content is 60%-70%. The fluorine-containing graphene quantum dot is smaller in size, uniform in morphology, stable in structure, high in singlet oxygen yield under visible light irradiation, extremely low in cytotoxicity, good in water solubility and more excellent in biocompatibility and is an ideal photosensitizer for photodynamic therapy and is suitable for the early treatmentprocess of esophagus cancer, skin cancer, lung cancer and the like and has a wide application prospect.