With the expect to research the influential factors to heat transfer property of waterborne polyurethane(WPU), synthesis and membrane properties of WPU are researched, to which the composition of monomers, such as the 2,4-toluene diisocynate(TDI), isophorone diisocyanate (IPDI), polypropylene glycol(PPG with Mn = 1000, 2000 g/mol), dimethylol propionic acid(DMPA) and small molecular ethylene glycol(EG) are discussed. The orthogonal experiments show that the order to affect the thermal conductivity is PPG > DMPA > R(-NCO/-OH). The differences in thermal conductivity of WPU membrane samples are expressed, wherein through DMA, DSC, TG, FTIR, AFM, and XRD analyzed. A fact that thermal conductivity has a strong correlation with crystallization behavior of WPU membrane samples. The crystallization behavior is dependent upon the degree of microphases separation between hard segment and soft segment and that all attribute to the short range, long range and microcrystalline ordering, similarly which that create a well free paths for phonon conduction and accompanying with the enhancement of heat conducting properties of WPU membranes.