We report the self-assembly behavior of graft polyurethanes combining in its structure soft lateral poly(n-butyl acrylate) (PnBuA) chains with rigid and crystallizable polycaprolactone (PCL) segments. Segmented polyurethanes microphase separated into high-glass transition temperature PCL hard and low-glass transition temperature PnBuA soft domains. The variation of the microstructure as a function of the hard segment content (ratio hard to soft segments) within the structure has been studied by using atomic force microscopy. Additionally, the crystallization mechanism appeared to be directly related to the properties of the substrates forming parallel lamellar structures on hydrophilic substrates and perpendicular lamellae with hydrophobic substrates.