The invention relates to a waterborne epoxy antirust coating for an urban rail and a bullet train body, and a preparation method thereof. The waterborne epoxy antirust coating comprises a basic coating and a film-forming resin, wherein the basic coating is prepared from a cross-linking agent, a pigment, an anti-rust pigment, a filler, a cosolvent, an accessory ingredient and water; the film-forming resin is prepared from a waterborne epoxy emulsion and an adhesion promoter. The waterborne coating is the coating with low VOC (Volatile Organic Compounds) and low toxicity, has no fire danger during construction, forms a film through mixed cross-linking of the basic coating and the film-forming resin, can play a role in protecting metals such as aluminum alloys and steel materials for locomotives and rail traffic, and has the characteristics of good adhesion on metal aluminum alloys and black metals for bullet trains, high corrosion resistance, and fast dryness; compared with a solvent type coating requiring to be added with 30 percent to 40 percent of organic solvent during spraying, the waterborne epoxy antirust coating adopts the water as a diluent, so that the discharge of VOC is greatly reduced during the spraying process, and the coating is environmental-friendly.