The invention discloses an aqueous epoxy modified alkyd resin and a preparation method thereof, and belongs to the chemical technology field. According to the aqueous epoxy modified alkyd resin, an epoxy resin serves as a modified material, an epoxy ester is synthesized through the reaction of the epoxy resin and a fatty acid, and the aqueous epoxy modified alkyd resin with good mechanical properties, water solubility, stabilities and rot resistance is synthesized through ester exchange of the epoxy ester and the alkyd resin. The aqueous epoxy modified alkyd resin is applied in aqueous industrial anticorrosion coatings, the manufactured aqueous industrial anticorrosion coatings have high adhesive force and hardness, good impact resistance and the like, no solvent exists in an aqueous industrial anticorrosion coating system, the discharge amount of volatile organic compounds (VOC) is low, and performances can reach or exceed performance indexes of similar solvent coatings. The aqueous epoxy modified alkyd resin has the advantages of being energy saving, environment friendly, capable of improving safeties of transportation and construction and suitable for large-scale popularization and application.