A series of multiblock polyurethane-ureas (PUU) based on polycaprolactone diol (PCL) with a molecular mass of 530 or 2000 g/mol, as well as hard segments of different lengths and structures, were synthesized by the step-growth polymerization method. The chemical structure of the synthesized multiblock copolymers was confirmed by IR- and NMR-spectroscopy. Differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) were used to determine the relaxation and phase transition temperatures for the entire series of the obtained PUU. The X-ray diffraction (XRD) method made it possible to identify PUU compositions in which the crystallizability of soft segments (SS) is manifested due to their sufficient length for self-organization and structuring. Visualization of the crystal structure and disordering of the stacking of SS with an increase in their molecular mobility during heating are shown using optical microscopy. The change in the size of the hard phase domains and the value of the interdomain distance depending on the PCL molecular mass, as well as the length and structure of the hard block in the synthesized PUU, were analyzed using small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). The evolution of the domain structure upon passing through the melting and crystallization temperatures of PUU soft blocks was studied using SANS. The studies carried out made it possible to reveal the main correlations between the chemical structure of the synthesized PUU and their supramolecular organization as well as thermal and mechanical properties.