Macromolecular diols with different carbamate content were synthesized by alterative n ((PPG))/n ((HMDI)) ratio. The molecular weights of these macromolecular diols were measured by GPC. In addition, based on these macromolecular diols, waterborne polyurethanes (WPU) were prepared by the pre-polymerization method. The structure and molecular weight of the WPU were characterized by (HNMR)-H-1, FTIR and GPC, respectively. When the mole ratio of n ((PPG)) and n ((HMDI)) decreased, the particle distribution of WPU became broader and the average particle size became larger. Furthermore, the hydrogen bonding interaction in WPU films was analyzed by the deconvolution of amino, carbonyl band and ether band of FTIR spectra. The results showed that when introduced carbamate into the macromolecular diol, the ordered hydrogen bonding interaction in hard segments increased and the interaction between carbamate and ether occurred. The increased hydrogen bonding interaction leads to the higher micro-phase separation confirmed by AFM and DSC test. Carbamate in soft segments can significantly increase the modulus of WPU in the whole temperature range. Meanwhile, the tensile strength and the elongation at break were obviously increased when introduced carbamate into the soft segments because of the crosslinked structure and micro-phase separation morphology. The tensile strength of sample WPU1 caught 28.28 MPa which was 2.37 times and the elongation at break caught 911% which was 2.18 times than that of WPU0.