The invention discloses corrosion-resistant water-based supramolecular polyurethane resin and a preparation method and application thereof. The preparation method comprises the following steps of: (1)uniformly mixing a polydiol and a carboxylic acid type hydrophilic diol, then adding diisocyanate and a catalyst, taking a solvent as a reaction medium, and reacting for 2 to 3 hours at 55 to 85 DEGC to obtain a mixed product I; (2) cooling to 50-70 DEG C, adding cyclodextrin or derivatives thereof into the mixed product I, reacting for 6-7 hours, cooling to 25-40 DEG C, and neutralizing to obtain a mixed product II; (3) adding water to the mixed product II for emulsification, adding a corrosion inhibitor for uniform mixing, and removing the solvent to obtain the corrosion-resistant water-based supramolecular polyurethane resin. The resin structure prepared by the invention contains the cyclodextrin which can improve the solubility of the oily corrosion inhibitor in water, and the bioavailability, the mechanical property and the stability of the compound, and the corrosion-resistant water-based supramolecular polyurethane resin is environment-friendly, and has wide application valueas basic resin of water-based anticorrosive coatings and adhesives.