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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 toward 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.