Polyurethane material is widely utilized in industry and daily life due to its versatile chemistry and relatively easy handling. Here, we focused on a novel thermally reversible cross-linked polyurethane with comprehensive remarkable mechanical properties as reported in our recent work (Adv. Mater. 2013, 25, 4912). The microphase-separated structure and heterogeneous segmental dynamics were well revealed by T-2 relaxometry experiments, which was also first utilized to in situ monitor the reversible cross-linking associated with Diels-Alder (DA) and retro-Diels-Alder (RDA) reactions. On the basis of T-2 relaxometry results, we determined the actual temperature of the (R)DA reaction as well as the corresponding activation energies of the motion of soft segments. Besides, the roles of the temperature and cross-linker contents on the microdomain structure and dynamics are discussed in detail. It is found that the microphase separation is enhanced by the increase of temperature as well as the incorporation of cross-linkers. Also, the polyurethane samples are still thermal-stable even at a high temperature beyond the disassociation of the cross-linkages. Furthermore, Baum-Pines and three-pulse multiple-quantum NMR experiments are utilized to investigate the heterogeneous structures and dynamics of the mobile and rigid segments, respectively. Both the results obtained from the T-2 relaxometry and multiple-quantum NMR experiments are in good agreement with the macroscopic mechanical properties of the polyurethane. Finally, it is also well demonstrated that proton T-2 relaxometry combined with multiple-quantum NMR is a powerful method to study the heterogeneous structures and dynamics of a multiphase polymer system.