Waterborne polyurethanes (WPUs) derived from polytetramethylene ether glycol (PTMG), 3-isocyanatomethyl-3,5,5-trimethylcyclohexyl isocyanate, 1,4-butanediol and dimethylolpropionic acid were synthesized. Hydroxyl-terminated polydimethylsiloxane (PDMS) was introduced to replace part of PTMG as soft segment. The effects of [-NCO]/[-OH] (R value) and PDMS content on structure and properties of WPU were studied using FTIR, thermal analysis, mechanical test, contacting angle testing and scan electron microscopy (SEM). The results revealed that the trend of particles fusion in WPU film decreased with the increment of R value by SEM photos. The replacement of PTMG by PDMS led to an obvious change in surface properties of films and distinct phase separation was observed by SEM photos when the PDMS content increased. This is the result when the content of PDMS was 2.0 wt% and R value is 1.2, the film exhibited excellent mechanical properties with the highest elongation at break and improved tensile strength.