The invention discloses water-based polyester resin for an amino baking coating. The water-based polyester resin is prepared from the following raw materials in parts by weight: neopentyl glycol, diethylene glycol, trimethylolpropane, glycidyl tertiary carbonate, 1,4-cyclohexane dicarboxylic acid, phthalic anhydride, hexahydrophthalic anhydride, isophthalic acid, 5-sulfoisophthalic acid monosodiumsalt, 1,4-butanediol-2-sodium sulfonate, xylene, a catalyst, a neutralizer, a cosolvent, a solvent and deionized water. The invention further discloses a synthesis device for the water-based polyester resin for the amino baking coating. The monomer of the water-based polyester resin for the amino baking coating prepared by the preparation method has good performance, and performance of the aminobaking coating prepared from the water-based polyester resin provided by the invention is superior to performance of amino baking coatings prepared from common water-based polyester resin in the market. According to the synthesis method for the water-based polyester resin for the amino baking coating, heating rods and a spiral heating pipe can be simultaneously used for heating from inside and outside, heating efficiency is improved, and production efficiency of the whole water-based polyester resin is improved.