Monoclinic ZrO2 was irradiated by 1.46 GeV Au ions using the UNILAC accelerator at the GSI Helmholtz Centre for Heavy Ion Research (Darmstadt, Germany), and the irradiated material was structurally characterized by high-resolution synchrotron X-ray and neutron total scattering experiments coupled with pair distribution function (PDF) analysis. The monoclinic-to-tetragonal phase transformation of swift heavy ion-irradiated ZrO2 has been widely studied, yet details of how irradiation drives the transformation proceeds at the atomic scale remain unclear. Using PDF analysis, we have probed the local structure of ZrO2 before and after irradiation to a fluence of 5×1012 and 1×1013 ions cm-2 and revealed that the long-range structure is described best using the previously reported tetragonal high-temperature phase; however, the local atomic arrangement cannot be fully described by this structural model alone at the level of because it cannot explain the observed nearest neighbor bonds and coordination polyhedra. A metastable, orthorhombic high-temperature phase, distinct from the monoclinic and tetragonal phases, must be included in the refinement of the local structure after ion irradiation. This phase was predicted but never observed because of its inherent metastable character in the structural transformation pathway between the monoclinic and tetragonal polymorphs but has never been experimentally confirmed. This orthorhombic phase, which quickly loses correlation beyond the nanoscale, is an essential ingredient to explain the structure of zirconia across the relevant range of length scales. This study contributes to an improved understanding of the mechanisms of the ion beam-induced crystalline-to-crystalline transformation polymorphism in ZrO2 and describes how orthorhombic structural building blocks organize across the mesoscale to yield the tetragonal long-range ZrO2 structure. Interestingly, this structural heterogeneity has also been reported in other complex oxides after swift heavy ion irradiation.