Polyester-based waterborne polyurethane (WPU) dispersions having poly(ethylene glycol) adipate diol, isophorone diisocyanate, and hexamethylene diisocyanate as the main raw materials were synthesized by an acetone process. In each step of the synthesis process, the intermediate products were collected, and the crystallization morphologies and relative crystallinity (X) of the soft segments (SSs) in their films were investigated by means of polarizing optical microscopy, differential scanning calorimetry, and X-ray diffraction. The fracture surfaces and thermostability of the intermediate films were also investigated by scanning electron microscopy (SEM) and TGA, respectively. The results show that the crystalline dimensions of the SSs decreased substantially during the synthesis process of WPU. X of the SSs decreased after the prepolymerization reaction and increased after the hydrophilic chain-extending reaction, then decreased after emulsification, and finally increased after the secondary chain-extending reaction. Moreover, The SEM photos indicate that with decreasing crystalline dimensions, the fracture mechanisms of the intermediate films varied gradually from brittle failure to ductile fracture. The thermostability of the intermediates obtained in each step of the synthesis process was in accordance with the variation tendency of the X of the SSs. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40270.