The invention belongs to the paint technical field, in particular relates to a waterborne polyurethane modified epoxy steel structure anti-corrosive paint and a preparation method thereof. The component A of the paint is a dispersion of modified E-20 and the component B used as curing agent is a waterborne dispersion which is prepared through modification by using epoxy and hydrophilic groups. The system has the advantages of common waterborne paints, overcomes the defects of the waterborne epoxy anti-corrosive paint and has the advantages of polyurethane and epoxy materials. The waterborne epoxy anti-corrosive paint prepared by using the system as the base material has great development prospect in the field of steel structures such as bridges, pipes, containers, industrial plants and public facilities.