The invention discloses a gingko beverage and a preparation method thereof, belonging to the technical field of processing of food beverages, and providing a novel process for preparing a gingko beverage by using a modern biotechnology. According to the gingko beverage and the preparation method thereof, by adopting conventional processes of shelling, cooking for detoxicating, removing endopleura, colloid-milling, homogenizing and the like and a modern enzymolysis technology, or a preparation method further matched with an enzymolysis technology and a probiotic fermentation technology, on the basis of preserving organic nutrients and flavor of gingko, the problems of high viscosity and poor taste of the gingko beverage are solved; the prepared gingko beverage is cool and fine in taste, delicious in sour and sweetness, relatively excellent in palatability, and stable in tissues; nutritional ingredients are relatively preferably absorbed by a human body; meanwhile, the gingko beverage is rich in effective ingredients such as abundant ginkgetin and ginkgo terpene lactones, and has a relatively excellent health function.