The invention discloses a novel black and red Chinese wolfberry fruit compound fermented beverage and a preparation method thereof and belongs to the processing field of microbial fermentation technologies of foods. The preparation method mainly comprises the steps of pretreatment of raw materials, juicing, ultrasonic assisted chitosan immobilized complex enzyme treatment, filtration, pasteurization, primary fermentation of a lactic acid bacterium composite leavening agent, secondary fermentation with active dry yeast and acetic acid bacteria, saccharic acid blending, centrifugation, pasteurization, filling and finished beverage. The preparation method is simple in process and low in processing cost, the prepared beverage has the flavor of Chinese wolfberry fruits and also has the smell produced through Chinese wolfberry fruit, a pleasant mellow aroma and soft sour, so that the beverage has more delicate taste, has no bad odor, homogeneous color and luster and good nutritional health-care functions; the total acid of the beverage is 2.83%, pH is 3.70, the aqueous protein of plants is 2.83g/L, the total phenol is 38.17mg/L, the carotenoid is 35.67ug/L, the alcoholic strength is 1% or below, and bacteria and escherichia coli are not detected out.