Polyurethane elastomer (PUE) excels in demanding applications due to its outstanding mechanical properties and environmental tolerance. Under compressive fatigue, viscoelastic dissipation induces significant heat accumulation, driving complex thermo-mechanical coupling and microstructural evolution that ultimately leads to failure. However, the dynamic response of PUE's hierarchical structure under such conditions remains elusive. To address this, we designed PUEs with low (LP) and high (HP) degrees of microphase separation. Through synchronized temperature-field monitoring and multiscale characterization, we deciphered the thermo-mechanically driven hierarchical structural evolution under cyclic compression. Key findings reveal that LP suffers severe early-stage heat buildup, promoting hard segment rearrangement into disordered domains. Subsequently, spherulites deform into ellipsoids, fragment, and finally melt, causing structural collapse and a high compression set (17.2%). In contrast, HP's well-ordered hard-segment network effectively distributes stress via lamellar reorientation, followed by progressive spherulite fragmentation. This mechanism preserves structural integrity, resulting in a superior fatigue durability and a low compression set (6.2%). This study unveils the thermo-mechanical evolution pathways of PUE's hierarchy for the first time, establishing a fundamental structure-property relationship to guide the design of high-fatigue-resistance elastomers.