The evolution of the microstructure and mechanical properties of low-energy heavy-ion-irradiated LiTaO3 crystals annealed at various temperatures was investigated by transmission electron microscopy (TEM) observations and nanoindentation tests to extend the applications of irradiated LiTaO3 crystals. Before annealing, randomly distributed voids formed in an approximately 200 nm thick region at the end of the ion irradiation range, which was attributed to preferential absorption of interstitials by the amorphous-crystalline interface. After annealing, a new directional diffusion path of defects was identified, resulting in a void string. Furthermore, void string diffusion to the free surface was also found during the annealing temperature increase process, which offers a potential application in designing custom sized-thickness exfoliation at the nanoscale. Meanwhile, two competing processes were identified during the annealing process: epitaxial recrystallization from the amorphous-crystalline interface and grain nucleation process in the amorphous region, which formed phases different from the matrix crystal structure, resulting in an interaction between them. Furthermore, the hardness of irradiated samples was also found to be affected by the annealing process; in particular, a hardness decrease induced by the interstitial Fe ions in the recrystallized region was also confirmed, which can improve the processability of samples for further application.