Although charged particle therapy, including carbon ion beam radiation, is a cutting-edge technology in human cancer treatment, the molecular mechanisms underlying cellular resistance to this type of therapy remain unknown. Furthermore, the chemotherapeutic agents that are most effective at overcoming cellular resistance remain unknown. In the present study, carbon ion beam radioresistant rodent cells were developed and their sensitization to trifluorothymidine (FTD), a derivative of deoxythymidine, was studied. The results of the present study demonstrated that carbon ion beam radioresistant cells were more sensitive to FTD compared with X-ray radioresistant cells. The results of the present study suggested that FTD is involved in carbon ion beam radioresistance, encouraging further study of cellular resistance to charged particle therapy for refractory human cancer.