The aim of this study was to investigate the damage of low-energy ions to HeLa cells and to particularly examine the relationship between apoptotic and necrotic effects and the low-energy ion radiation. In this study, HeLa cells were irradiated by low-energy ions (30keV N+) at different doses. The level of apoptosis and necrosis was evaluated using flow cytometry. Since vacuum is required for experimental low-energy ion generation and irradiation, the cells must be placed in vacuum. Mineral oil was used to prevent dehydration of cells. The results show that the apoptotic rate reached 7.09% when the ion implantation dose was 1 × 1015 ions/cm2; and when the cells were exposed to and implanted at 2 × 1015 ions/cm2 dose, the apoptotic rate was higher than that at 1 × 1015 ions/cm2, and the necrotic rate was 15.63%. In addition, the survival fraction gradually decreased with the increase in implantation dose. Some relationships have been found between the radiation-induced apoptosis and the incubated time after irradiation.