The structural evolution of multiblock thermoplastic polyurethane ureas based on two polydiols, poly(1,4-butylene adipate (PBA) and poly-ε-caprolactone (PCL), as soft blocks and two diisocyanites, 2,4-toluylene diisocyanate (TDI) and 1,6-hexamethylene diisocyanate (HMDI), as hard blocks is monitored during in situ deformation by small- and wide-angle X-ray scattering. It was shown that the urethane environment determines the crystal structure of the soft block. Consequently, two populations of crystalline domains of polydiols are formed. Aromatic TDI forms rigid domains and imposes constrains on the crystallization of bounded polydiol. During stretching, the TDI–polydiol domains reveal limited elastic deformation without reorganization of the crystalline phase. The constrained lamellae of polydiol form an additional physical network that contributes to the elastic modulus and strength of the material. In contrast, polydiols connected to the linear semi-flexible HMDI have a higher crystallization rate and exhibit a more regular lamellar morphology. During deformation, the HMDI-PBA domains show a typical thermoplastic behavior with plastic flow and necking because of the high degree of crystallinity of PBA at room temperature. Materials with HMDI-PCL bonding exhibit elastic deformation due to the low degree of crystallinity of the PCL block in the isotropic state. At higher strain, hardening of the material is observed due to the stress-induced crystallization of PCL.