The invention relates to the technical field of adhesives, in particular to an anti-skinning waterborne polyurethane adhesive and a preparation method thereof. The anti-skinning waterborne polyurethane adhesive is prepared from the following raw materials in parts by weight: 95-99 parts of a waterborne polyurethane dispersoid, 0.1-0.5 part of a wetting agent, 0.1-0.5 part of an antifoaming agent and 0.1-1 part of a thickening agent, wherein the waterborne polyurethane dispersoid is prepared from the following raw materials: polyol, inorganic mineral powder, polyisocyanate and a carboxyl chainextender in a molar ratio is 1:(0.1-0.6):(2-5):(0.2-2). According to the anti-skinning waterborne polyurethane adhesive and the preparation method thereof, reaction between the inorganic mineral powder and the polyisocyanate is carried out, the prepared waterborne polyurethane dispersoid cannot completely enclose the active groups of the inorganic mineral powder, and certain water-retaining groupsof the inorganic mineral powder are retained, so that the generation of skinned adhesive films of the waterborne polyurethane adhesive skinning is inhibited.