Bio‐based polyurethanes (PU) containing poly(ε‐caprolactone) diol (PCL) and hydroxyl telechelic natural rubber (HTNR) were synthesized. The effect of the diisocyanate structure and the molecular weights of diols on the mechanical properties of PU were investigated. Three different molecular structures of diisocyanate were employed: an aliphatic diisocyanate (hexamethylene diisocyanate, HDI), an aromatic diisocyanate (toluene‐2,4‐diisocyanate, TDI) and a cycloalkane diisocyanate (isophorone diisocyanate, IPDI). Two molecular weights of each diol were selected. When HDI was employed, a crystalline PU was generated while asymmetrical structures of TDI and IPDI provided an amorphous PU. The presence of crystalline domains was responsible of a change in tensile behavior and physical properties. PU containing TDI and IPDI showed a rubber‐like behavior: low Young's modulus and high elongation at break. The crystalline domains in PU containing HDI acted as physical crosslinks, enhancing the Young's modulus and reducing the elongation at break, and they are responsible of the plastic yielding. The crystallinity increased the tear strength, the hardness and the thermal stability of PU. There was no significant difference between the TDI and IPDI on the mechanical properties and the physical characteristics. Higher molecular weight of PCL diol changed tensile behavior from the rubber‐like materials to the plastic yielding. Thermal and dynamic mechanical properties were determined by using DSC, TGA and DMTA. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013