Three series of shape memory poly(ester-urethane) with varying hard-segment contents were synthesized. The materials were designed to display a three-phase structure consisting of a disperse phase formed by crystallites and hard domains embedded in an amorphous matrix. The initial undeformed morphology was investigated using techniques such as modulated differential scanning calorimetry, Fourier transform infrared spectroscopy, and wide angle X-ray scattering. These techniques were used to determine the phase separation, hydrogen-bonding structure, and crystalline fraction of the specimens prior to thermo-mechanical treatments. The obtained information was correlated with small angle X-ray scattering investigations of morphological changes that occurred during shape memory cycling. The deformation cycle led to the formation of an oriented nanostructure derived from chain alignment. The nanostructure recovered was observed to be triggered by the melting of the crystallites and bulk incompatibility. A relationship between the ability of the studied poly(ester-urethane) specimens to recover their original shape and their original nanostructure was determined.