This work reports the study on the evolution of native defects in ZnO nanorods irradiated with hydrogen ion. ZnO nanorod arrays grown vertically on silicon substrates were irradiated by 180 keV H+ ions to a total fluence of 8.50 × 1015 ions/cm2. The X-ray diffraction spectra, photoluminescence spectra before and after irradiation and the real-time ionoluminescence spectra of the nanorod arrays during the irradiating process were measured. Formation and evolution of defects during H+ ion irradiation and effects of irradiation on the crystal structure and optical property were studied. Blue shift of exciton emission, shrink of lattice c and improvement of the crystallinity of ZnO nanorods after irradiation were observed. Simple surface passivation of the nanorods could improve the radiation resistance. Formation and evolution of the defects during H+ ion irradiation could be clarified into four stages and the related models are provided.