The invention relates to a method for preparing hyperbranched waterborne polyester resin which is composed of, by weight, 6-10% of TMP, 15-20% of DMPA, 0.1-0.5% of p-toluene sulfonic acid, 15-25% of neopentyl glycol, 12-20% of m-phthalic acid, 20-30% of maleic anhydride or phthalic anhydride, 6-10% of adipic acid, 0.1-0.5% of p-methoxyphenol, 20-30% of ethylene glycol monobutyl ether, 12-20% of dimethylethanolamine, and 70-130% of deionized water. The prepared hyperbranched waterborne polyester resin has the advantages of excellent hydrolysis resistance, water dispersibility and storage stability, has the characteristics of high glossiness, good abrasion resistance, strong adhesion powder, high fullness, excellent impact resistance and the like no matter the resin is made into a waterborne stoving varnish with amino resin or is made into a waterborne woodware paint with hydrophilic polyisocyanate, and is widely used in surface coating and protection of woodware, metals, zinc alloys, aluminum alloys, magnesium alloys, plastics and other products,.