The invention discloses water-based amino stoving varnish and a preparation method thereof, and relates to the technical field of coating compositions. The water-based amino stoving varnish is prepared from, by weight, 25%-40% of water-based polyester resin, 4%-5% of water-based epoxy resin,7%-10% of water-based amino resin, 25%-35% of deionized water, 1.5%-2.5% of pH modifier, 0.3%-0.5% of wetting agent, 0.2%-0.6% of antifoaming agent, 0.5%-1% of dispersing agent, 1%-5% of cosolvent, 10%-20% of pigments and filler, 2%-5% of nanometer aluminum oxide, 0.3%-0.5% of magnesium lithium silicate, 0.3%-0.5% of thickener and 0.5%-0.8% of flatting agent through uniform mixing and stirring. The flatting agent is waterborne, environmentally friendly, good in stability, high in hardness, high in adhesive force, fast in drying, high in gloss retention, excellent in ageing resistance, good in water resistance, convenient to construct, low in cost and free of pollution.