Knowledge of radiation-induced structural changes in complex oxides is of technological importance for the development of container materials for the immobilization of nuclear waste. Fluorite structural derivatives are candidates for container materials, but their disordering processes under radiation environments are still unclear. In the present study, ion irradiation was performed on the Sc2O3-HfO2 pseudo-binary system in which fluorite-related structural compounds such as β-Sc2Hf7O17, γ-Sc2Hf5O13, and δ-Sc4Zr3O12 exist, and the short-range ordered structures were investigated by transmission electron microscopy (TEM). The pristine long-range ordered rhombohedral phase was found to transform into a long-range disordered cubic oxygen-deficient fluorite phase upon ion irradiation. The atomic arrangements are not completely disordered, but a more ordered structure was present in the disordered fluorite matrix. A characteristic diffuse scattering was observed in the electron diffraction patterns, and dark-field TEM observations revealed that it is due to microdomains, defined as small regions where the degree of order is higher than that of the disordered matrix. Although the parent phase was different before irradiation, the short-range organization is the same. A comparison of diffuse scattering with the location of superlattice reflections suggested that the microdomains have a structure similar to the δ-phase. With increasing Sc2O3 concentration, the microdomains of δ-type structures were suggested to change to short-range ordered bixbyite structures, which are not present in the 2 equilibrium phase diagram.