The invention discloses a waterborne epoxy anti-corrosive coating and a preparation method thereof. The coating comprises a component A and component B, wherein the component A comprises high titanium ash, feldspar powder, silicon carbide, ceramic fine powder, a nanometer silicon dioxide solution, zinc phosphate, water and the like; and the component B is a waterborne epoxy curing agent. The preparation method comprises the following steps of: adding a waterborne epoxy resin and a waterborne dispersing agent into a reaction kettle, starting a dispersing machine, adding the high titanium ash, feldspar powder, silicon carbide, ceramic powder, nanometer silicon dioxide solution, zinc phosphate and water in sequence, and dispersing; treating with a sand grinding machine; and adding auxiliary materials such as a waterborne antifoaming agent, a waterborne flatting agent and the like, and stirring to obtain a bottom and top-combined thick film waterborne epoxy anti-corrosive coating. The coating provided by the invention is corrosion resistant and wear resistant after one-time molding, the coating requirement of the inner wall of a steel structure bridge steel box girder is met, and the coating technical requirements of a plurality of severely-corrosive indoor steel structure platforms are met.