Thermoresponsive shape memory polymers (SMPs) have garnered increasing interest for their exceptional ability to retain a temporary shape and recover the original configuration through temperature changes, making them promising in various applications. The SMP shape change and recovery that happen due to a combination of mechanical loading and appropriate temperatures are related to its particular microstructure. The deformation process leads to the formation and growth of micro-cracks in the SMP structure, whereas the subsequent heating over its glass transition temperature Tg leads to the recovery of its original shape and properties. These processes also affect the SMP microstructure. In addition to the observed macroscopic shape recovery, the healing of micro-crazes and micro-cracks that have nucleated and developed during the loading occurs. Therefore, our study delves into the microscopic aspect, specifically addressing the healing of micro-cracks in the cyclic loading process. The proposed research concerns a thermoplastic polyurethane shape memory polymer (PU-SMP) MM4520 with a Tg of 45 °C. The objective of the study is to investigate the effect of the number of tensile loading-unloading cycles and thermal shape recovery on the evolution of the PU-SMP microstructure. To this end, comprehensive research starting from structural characterization of the initial state and at various stages of the PU-SMP mechanical loading was conducted. Dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), wide-angle X-ray scattering (WAXS) and scanning electron microscopy (SEM) were used. Moreover, the shape memory behavior in the thermomechanical loading program was investigated. The obtained average shape fixity value was 99%, while the shape recovery was 92%, which confirmed good shape memory properties of the PU-SMP. Our findings reveal that even during a single loading-unloading tension cycle, crazes and cracks nucleate on the surface of the PU-SMP specimen, whereas the subsequent temperature-induced shape recovery process carried out at the temperature above Tg enables the healing of micro-cracks. Interestingly, the surface of the specimen after three and five loading-unloading cycles did not exhibit crazes and cracks, although some traces of cracks were visible. The traces disappeared after exposing the material to heating at Tg + 20 °C (65 °C) for 30 min. The crack closure phenomenon during deformation, even without heating over Tg, occurred within three and five subsequent cycles of loading-unloading. Notably, in the case of eight loading-unloading cycles, cracks appeared on the surface of the PU-SMP and were healed only after thermal recovery at the particular temperature over Tg. Upon reaching a critical number of cycles, the proper amount of energy required for crack propagation was attained, resulting in wide-open cracks on the material's surface. It is worth noting that WAXS analysis did not indicate strong signs of typical highly ordered structures in the PU-SMP specimens in their initial state and after the loading history; however, some orientation after the cyclic deformation was observed.