The invention relates to a water-borne glass baking paint which is characterized by comprising the following components by the weight percentage: 20-60% of water-borne epoxy resin, 10-40% of low methyl etherified amino resin, 0-18% of water-borne acrylic resin modified polyurethane, 3-30% of a color concentrate dye or colorant, 0.1-0.8% of a leveling agent, 0.1-1.0% of a wetting agent, 0.1-0.8% ofan adhesive agent, 0.1-0.8% of an antioxidant, 0.1-0.6% of a defoamer, 0.1-0.4% of a bactericide, 0.5-6% of a pH regulator, and the balance being deionized water. The invention also discloses a preparation method of the water-borne glass baking paint. Compared with the prior art, the water-borne glass baking paint has good adhesion force on glass and other substrates, excellent alcohol resistance, excellent water resistance, excellent wear resistance, and no need of use of additional organic solvents. The preparation method is simple and environmentally friendly.