A series of solvent-free waterborne polyurethanes (WPUs) with different soft segment structure were prepared by respectively using different number-average molecular weight (Mn) of polytetramethylene glycol (PTMG, Mn = 1000, 2000, 3000) and poly (1,4-butylene adipate) (PBA, Mn = 1000, 2000 3000) as main diol in this paper. Effect of soft segment crystallization on water resistance of WPUs was discussed. The crystallization properties of WPU films were investigated by differential scanning calorimetry (DSC) and X-ray diffraction (XRD). The water resistance was determined by water absorption ratio. DSC and XRD results confirm that there are no crystalline structures in the WPU films which are synthesized with PTMG (Mn = 1000, 2000, 3000) and PBA (Mn = 1000), while the WPU films synthesized with PBA (Mn = 2000 and 3000) have obvious crystalline structures at room temperature. Meanwhile, the WPU films synthesized with PBA (Mn = 2000 and 3000) possess excellent water resistance because the existence of crystalline structure.