Background: Heavy ion radiation constitutes a major health risk for astronaut in space flight, potential damage to healthy tissues surrounding the tumor target along its penetrating path should still be considered in hydrotherapy. Therefore, there is a demand for reliable countermeasure against heavy ions radiation. In this study, we will estimate the radiomitigative effect of CpG-ODN on immune tissues after carbon ions radiation (CIR). Methods: Firstly, the 30 days’ survival of mice was observed, peripheral blood cell was counted, the injury of three principal immune tissues (including bone marrow, thymus and spleen) was evaluated by histological examination, apoptosis and double strand breaks (DSB) were detected by TUNEL staining and γ-H2AX immunohistochemistry respectively, and cytokine (G-CSF, IL-6 and TNF-α) was measured by ELISA assay. Results: the 30 days’ survival improved, the injury of three principal immune tissues were obviously ameliorated, the number of γ-H2AX foci and TUNEL-positive nuclei decreased, and G-CSF, IL-6 and TNF-α expression increased by CpG-ODN treatment after CIR. Conclusion: CpG-ODN could enhanced mice survival, and ameliorate immune tissues injury, the mechanism may be that CpG-ODN induced cytokines production and inhibited the double strand breaks (DSB) and apoptosis in order to stimulate the generation and mobilization of the immune cells and reestablish immune system to combat bacterial infections.