Complex oxides have attracted attention as a candidate for nuclear waste immobilization materials to replace borosilicate glass. Knowledge of radiation-induced structural changes is of technological importance for developing the container materials. In this study, we performed 94 MeV Pb ion irradiation into β-Sc2Hf7O17 and γ-Sc2Hf5O13 pellets at room temperature, and examined their structural changes by grazing x-ray diffraction (GIXRD) and transmission electron microscopy (TEM). Polycrystallization occurs at the surface of β-Sc2Hf7O17, while the crystallinity was maintained in γ-Sc2Hf5O13: the former was more susceptible to radiation damage than the latter. The ordered rhombohedral β- and γ-phases transformed to disordered cubic fluorite phase with increasing ion fluence. A domain structure was observed in β-Sc2Hf7O17, and the interface between the ordered and disordered regions was found to be related to the domain boundary.