A series of polyurethane elastomers (PUEs) based on 4,4′-cyclohexamethylene diisocyanate (H12MDI)/1,2-ethanediol as hard segment with the soft segments having different molecular weights of polycaprolactone diols, were effectively polymerized by two step technique. The structural characterization was performed by FT-IR spectroscopy. The X-ray diffraction (XRD) technique was used to study the crystallinity and hydrophilicity of the prepared polymer films. It was found that crystallinity and hydrophilicity increased with increasing the chain length of soft segments. The effect of molecular weight of polyols on the contact angle, water absorption (%) and swelling behavior of the synthesized polyurethanes were also studied. Moreover, the scanning electron microscopy (SEM) and atomic force microscopy (AFM) techniques revealed that the degree of micro-phase separation increases with increasing molecular weight of polyol which confirmed the results pattern shown by XRD diffractogram.