Polycarbonate diol-based waterborne polyurethane (WPU) was prepared by prepolymer mixing process. The prepolymer mixture contained the polycarbonate diol, isophorone diisocyanate (IPDI), dimethylol propionic acid, triethylamine, and ethylenediamine (EDA). The NCO/OH ratio in the prepolymer was adjusted by controlling the molar ratio of IPDI, and its effects on the properties of WPU were studied. The structure of WPU was characterized by fourier transform infrared spectroscopy. The average particle size increased and viscosity decreased with increasing NCO/OH ratio and EDA content in WPU. The reduced phase separation between soft and hard segments increased glass transition temperature. The reduction in the thermal decomposition temperature could be attributed to the low bond energy of urethane and urea groups, which constituted the hard segment. Additionally, the polyurethane chain mobility was restricted, elongation decreased, and tensile strength increased. The hydrogen bond between the hard segments formed a dense structure that hindered water absorption