The invention discloses a preparation method of a natural enzymatic hydrolysis reaction flavored milk and an application thereof in milk type essence, and the preparation method comprises the following steps: adding whey powder into a reactor container, adding pure water, and slowly stirring to obtain a substrate; carrying out enzymatic hydrolysis on the substrate under the stirring state, wherein the initial pH of the enzymatic hydrolysis is 8-10, the adding amount of enzyme is 0.5%-1.5% of the weight of the whey powder, the enzymatic hydrolysis temperature is 50 DEG C-70 DEG C, and the enzymatic hydrolysis time is 4-6 hours; and carrying out inactivation after the enzymatic hydrolysis is finished, then cooling, filtering and removing impurities till the temperature of material liquid is reduced to below 50 DEG C, obtaining enzymatic-hydrolyzed whey powder liquid, adding full-cream milk powder, glucose, lactose, natural amino acids, glycerol and water into the whey powder liquid, slowly heating to 80 DEG C, keeping the temperature for reaction for 3-5 hours, then adding pectin and obtaining the natural enzymatic hydrolysis reaction flavored milk. The obtained flavored milk is notonly stable, but also thick in natural milk flavor. The natural enzymatic hydrolysis reaction flavored milk can be applied in the production of Maillard peptide for the milk type essence.