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It is widely accepted that the interaction of swift heavy ions with many complex oxides is predominantly governed by the electronic energy loss that gives rise to nanoscale amorphous ion tracks along the penetration direction. The question of how electronic excitation and electron–phonon coupling affect the atomic system through defect production, recrystallization, and strain effects has not yet been fully clarified. To advance the knowledge of the atomic structure of ion tracks, we irradiated single crystalline SrTiO₃ with 629 MeV Xe ions and performed comprehensive electron microscopy investigations complemented by molecular dynamics simulations. This study shows discontinuous ion-track formation along the ion penetration path, comprising an amorphous core and a surrounding few monolayer thick shell of strained/defective crystalline SrTiO₃. Using machine-learning-aided analysis of atomic-scale images, we demonstrate the presence of 4–8% strain in the disordered region interfacing with the amorphous core in the initially formed ion tracks. Under constant exposure of the electron beam during imaging, the amorphous part of the ion tracks readily recrystallizes radially inwards from the crystalline-amorphous interface under the constant electron-beam irradiation during the imaging. Cation strain in the amorphous region is observed to be significantly recovered, while the oxygen sublattice remains strained even under the electron irradiation due to the present oxygen vacancies. The molecular dynamics simulations support this observation and suggest that local transient heating and annealing facilitate recrystallization process of the amorphous phase and drive Sr and Ti sublattices to rearrange. In contrast, the annealing of O atoms is difficult, thus leaving a remnant of oxygen vacancies and strain even after recrystallization. This work provides insights for creating and transforming novel interfaces and nanostructures for future functional applications.