Oxygen-deficient compounds A4B3O12 have a δ-type structure with a regular long-range arrangement of oxygen vacancies induced by compensation of the charge difference between A 3+ and B 4+ cations, while A and B cations do not order long-range and only display weak short-range correlations. The δ-type compounds in the Sc2O3-HfO2 and Sc2O3-ZrO2 systems exhibit excellent resistance to radiation-induced amorphization, but the long-range ordered δ-phase was transformed into a short-range ordered bixbyite phase. Since this structural change was not predicted from the phase diagram, the validity of the formation of the bixbyite phase and its stability are still unclear. In the present study, the changes of radiation-induced microstructures in δ-Sc4Hf3O12 under heat treatments and electron beam irradiations were examined by ex-situ and in-situ transmission electron microscopy. It was found that the ion-beam-induced metastable bixbyite phase is transformed into the δ and fluorite phases by the rearrangement of the oxygen vacancies.