The super-molecular structure and morphology of shape-memory polymers (SMP) have an evident influence on the shape-memory effect (SME). More detailed information on these structure-function relations during the dynamic processes of programming and shape recovery are required to better understand the SME. Here we explore whether wide and small angle x-ray scattering (WAXS, SAXS) in combination with deformation experiments can help to characterize and better understand the respective materials super-molecular structure (spatial organization of chain segments in crystalline and non-crystalline regions, characterized by parameters such as crystallinity, crystallite-sizes, domain-sizes and -arrangements) and its changes upon varying mechanical loads and temperature increase as stimulus. Multiphase polymer networks based on poly(ε-caprolactone) and poly(cyclohexyl methacrylate), whose molecular structures allow formation of at least two separated domains, were investigated using WAXS and SAXS, to describe the respective super-molecular structures and morphologies and their development during cyclic, thermomechanical tensile tests reproducing key features of shape-memory programming and recovery. The creation of the triple-shape capability for this AB polymer network system is performed by a one-step process, which is similar to a conventional dual-shape programming process. It could be shown via SAXS that a long period between crystalline domains exists for these polymer networks. The value of this long period changes by some nanometers as a consequence of programming and the resulting elongation of the respective sample. Further insights could be obtained by investigating WAXS diffraction peaks, detected at different steps during the thermomechanical treatment. It could be shown that crystal sizes in this polymer system remain unaffected by the programming process, while the crystallization of the stretched samples during the cooling process leads to a spatial rearrangement (preferential orientation) of crystalline domains.