Irradiating solid materials with energetic ions are extensively used to explore the evolution of structural damage and specific properties in structural and functional materials under natural and artificial radiation environments. Lithium niobate on insulator (LNOI) technology is revolutionizing the lithium niobate industry and has been widely applied in various fields of photonics, electronics, optoelectronics, etc. Based on 30 MeV 35Cl and 40Ar ion irradiation, thermal spike responses and microstructure evolution of LNOI under the action of extreme electronic energy loss are discussed in detail. Combining experimental transmission electron microscopy characterizations with numerical calculations of the inelastic thermal spike model, discontinuous and continuous tracks with a lattice disorder structure in the crystalline LiNbO3 layer and recrystallization in the amorphous SiO2 layer are confirmed, and the ionization process via energetic ion irradiation is demonstrated to inherently connect energy exchange and temperature evolution processes in the electron and lattice subsystems of LNOI. According to Rutherford backscattering/channeling spectrometry and the direct impact model, the calculated track damage cross–section is further verified, coinciding with the experimental observations, and the LiNbO3 layer with a thickness of several hundred nanometers presents track damage behavior similar to that of bulk LiNbO3. Systematic research into the damage responses of LNOI is conducive to better understanding and predicting radiation effects in multilayer thin film materials under extreme radiation environments, as well as to designing novel multifunctional devices.