A series of waterborne polyurethane adhesives (WPUAs) were prepared from diphenylmethane-4,4 0 -diisocyanate (MDI), 1,6-hexamethylene diisocyanate (HDI), poly(1,4-butanediol adipate) diol (PBA), 1,4-butanediol (BDO), and internal-emulsifying agents by the prepolymer mixing method. The viscosity, mechanical properties, thermal properties, and adhesion strength of the samples were measured. The structure-property relationship was discussed primarily. The results indicated that the MDI/HDI and PBA/BDO molar ratio influenced these properties. The WPUA exhibited excellent T-peel strength and mechanical properties at a suitable MDI/ HDI (or PBA/BDO) molar ratio. Moreover, higher MDI/ HDI (or PBA/BDO) molar ratio resulted in higher thermal stability.