The invention discloses a waterborne polyurethane adhesive and a preparation method thereof. The waterborne polyurethane adhesive is obtained by synthesizing raw materials such as polyester polyol, castor oil, isocyanate, a hydrophilic extended chain agent, organosilane, a salt forming agent, a solvent, a catalyst and deionized water. The polyester polyol and the castor oil with high water resistance are used, the castor oil is a polyether substance with lyophobic structure and the internal crosslinking structure of silane is adopted, so that the water resistance of the waterborne polyurethane adhesive is enhanced greatly; after an ammonia silane coupling agent is added, an amidogen reacts with residual isocyanate and a hydrolysable silica group undergoes hydrolytic polycondensation so asto perform crosslinking and chain extension on a system; and glue prepared by the process has high bonding strength and high water resistance and can meet the performance requirement of the waterborne polyurethane adhesive.