Ionizing radiation kills cells mainly due to the generation of DNA double-strand breaks (DSBs). High-linear energy transfer (LET) ionizing radiation induces more cell death and generates a higher relative biological effect (RBE) than low-LET ionizing radiation (such as X or γ ray). Although it is known that interference with the Ku-dependent nonhomologous ending-joining (NHEJ) pathway appears to be the major cause of iron-ion- and carbon-ion-induced cell death, it remains unclear whether other ions with a similar or different LET and higher RBE in terms of cell killing are controlled in the same way. In this study, we compared the clonogenic survival frequency of Ku80+/+ (NHEJ-proficient) and Ku80-/- (NHEJ-deficient) cells after exposure to iron (175 keV/μm), silicon (75 keV/μm), oxygen (25 keV/μm) and X ray (low-LET). The results showed that Ku80-/- cells had the same RBE value of 1 for cell killing for all types of ionizing radiation, whereas Ku80+/+ cells had different RBE values for cell killing that depended on the specific type of ionizing radiation. The results indicate that the Ku-dependent NHEJ is the major repair pathway that heavier ions interfere with, resulting in higher RBE for cell killing. These results provide useful information for followup studies that will focus on improving high-LET protection or heavier ion radiotherapy in the near future.