The aliphatic waterborne polyurethaneureas (WPU) with different isocyanate index (R) were synthesized by isophorone diisocyanate (IPDI) and polyester glycol via prepolymer mixing method. The effects of the R value on the structure and the properties of the resultant polymers have been analyzed. The polymer with a certain R value (R = 1.44) exhibited excellent mechanical properties with both high tensile strength (55 MPa) and high elongation at break (1400%). The water resistance and the thermal stabilities of WPUs have been improved with the increase of R. The results were interpreted in terms of the structures associated with the micro-phase separation. According to differential scanning calorimeter (DSC) analysis, the microphase separation degree was elevated by increasing R value. FTIR spectrum showed the more R value, the more hydrogen bonded urea groups. No crystallinity was found in X-ray diffraction (XRD) patterns showing the typical amorphous morphologies of IPDI-based WPUs. Thus the primary driving force for microphase separation was the hydrogen bonding between urethane and urea groups, making significant influence on the properties of WPUs, as shown in dynamic mechanical analyzes. (C) 2010 Wiley Periodicals, Inc. J Appl Polym Sci 118: 920-927, 2010