The invention belongs to the technical field of hot melt adhesives, and discloses a waterborne polyurethane hot melt adhesive as well as a preparation method and application thereof. The preparation method comprises the following steps: (1) adding polyether polyol in a reaction kettle, heating to 120-130 DEG C, and carrying out heat preservation, water removal and cooling; (2) under the condition of stirring, dropwise adding a catalyst into the reaction kettle and then adding polyisocyanate, heating to 80-88 DEG C, and carrying out a heat preservation reaction to obtain a mixture; (3) dropwise adding a carboxylic monomer solution into the mixture, adjusting the temperature, and carrying out heat preservation reaction to obtain a crude product; (4) adding acetone into the crude product, increasing the rotating speed of a stirrer, cooling to 35-40 DEG C, adding a neutralizing agent for neutralization, taking out the obtained material, adding distilled water, and conducting high-speed shearing emulsification and rotating evaporation to obtain the waterborne polyurethane hot melt adhesive. The waterborne polyurethane hot melt adhesive provided by the invention is low in melt temperature, and high in solid content and stripping force, and remains in a liquid state at normal temperature; meanwhile, the preparation method is mild in reaction condition and low in energy consumption; the waterborne polyurethane hot melt adhesive is applied to the field of adhesives.