The invention discloses a preparation method of an apple enzyme functional beverage, and belongs to the technical field of food. The preparation method comprises the steps of taking apples, white granulated sugar and purified water as raw materials, inoculating a fermentation preparation for three times of fermentation in sequence, firstly inoculating saccharomyces cerevisiae with the inoculationamount of 0.1-0.2%, fermenting for 5 d, and sterilizing; inoculating Acetobacter pasteurianus with the inoculation amount of 1.2-1.8%, fermenting for 3 d, and sterilizing; finally inoculating lactobacillus plantarum with the inoculation amount of 1.2-1.8%, fermenting for 4 days, and sterilizing. Compared with the gamma-aminobutyric acid prepared by simultaneous fermentation of the three bacteria,the content of the gamma-aminobutyric acid is low, and the content of total phenols and crude polysaccharides is high. The apple enzyme functional beverage disclosed by the invention is wide in raw material source, low in price, unique in sweet and sour taste and mellow in mouthfeel; the product has stable quality, no preservative, rich metabolite and easy absorption by human body. The apple enzyme functional beverage can clear toxins in the body, clear free radicals, delay aging, resist cancer, maintain beauty and keep young, enhance memory and improve immunity.