The invention discloses a water-based baking paint for a glass substrate and a preparation method and the application thereof; the formula of the water-based glass baking paint comprises the following components in parts by weight: 45 to 63 percent of water-soluble acrylic resin, 5 to 7 percent of methylated amino resin, 5 to 15 percent of water-based paste, 1.2 to 1.5 percent of coupling agent, 2 to 5 percent of additive and 25 to 30 percent of deionized water. When the baking paint is prepared, first the water-soluble acrylic resin, defoamer, wetting agent, leveling agent, dispersant and some water are sequentially added into a stirring tank to be stirred, is added with the water-based slurry and the like to be stirred and dispersed at high speed; and finally the methylated amino resin, the coupling agent and the rest water are sequentially added in to be stirred into a uniform coating system. The invention also provides a use method of the glass baking paint. When being applied to ground glass, hard glass and other substrates, the coating has the advantages of simple preparation process, convenient construction, strong coating adhesion, high hardness, water resistance, good heat resistance and the like.