Swift heavy ion irradiation was carried out to examine the ionization effects on structural changes of δ-Sc4Hf3O12 in which oxygen vacancies are regularly arranged. The specimens were irradiated at room temperature with 92 MeV xenon ions to fluences ranging from 3×1012 to 1×1014 /cm2, and characterized by grazing (glancing) incidence x-ray diffraction, transmission electron microscopy, and scanning transmission electron microscopy. It was found that the pristine long-range ordered rhombohedral δ-phase undergoes a reconstructive transformation towards a long-range disordered cubic oxygen-deficient fluorite phase promoted by ionization effects. In addition, an ordered phase with a short-range structure different from the δ-type was formed in a layer going from the surface to a depth of ~4.5 µm in the specimen irradiated to a fluence of 1×1014 /cm2. It was found that the ordered phase is formed from the disordered cubic fluorite phase. This structural change is anomalous, because it is the opposite process of the usual irradiation-induced structural change, the order-to-disorder phase transformation. Electron diffraction experiments revealed that short-range ordered regions in this layer possess an oxygen-excess bixbyite organization (C-type heavy rare-earth oxides) with randomly filled anion vacant sites to account for the different stoichiometry, and a long-range average oxygen-deficient fluorite phase.