The invention relates to a waterborne polyurethane adhesive for an RFID antenna substrate. The adhesive comprises polyurethane emulsion, a waterborne curing agent and a filler, and the composition according to weight percentage is as follows: 45%-65% of polyurethane emulsion, 25%-35% of waterborne curing agent, 5%-20% of filler, 0.2%-0.6% of deformer and 0.3%-0.7% of stabilizer, wherein the polyurethane emulsion comprises polyol, diisocyanate, a chain extender and an organic solvent, a prepolymer as shown in formula (II) is obtained by polycondensation in the presence of an organic tin type catalyst, m in the formula is equal to 1-100, and the formula (II) is dispersed in water containing an emulsifier, thereby preparing the emulsion with the solid content of 20-50% by weight. The adhesive is used for adhering a paper thin film or a polyester thin film with an aluminum foil or a copper foil. A prepared polyester or paper-based aluminum-coated plate and a polyester or paper-based copper-coated plate can be used for the RFID antenna substrate, and have high peeling strength, good acid and alkali resistance, good storage stability, excellent comprehensive performance and low cost.