The invention discloses a functional papaya compound beverage and a preparation method thereof. The preparation method is characterized by using fresh papayas as main raw materials, using honeysuckle flowers, chrysanthemums, mulberry leaves, cogongrass rhizomes, lophatherum gracile and Canton love-pea vines as auxiliary materials and then adding honey, edible additives and water, wherein the percents by weight of the components are as follows: 5-90% of raw papaya juice or papaya juice composed of papayas and water, 2-90% of Chinese herbal medicine mixed condensed juice, and 0.05-20% of honey, edible additives and water. The preparation method comprises the following specific steps: selecting papayas, cleaning, peeling, deseeding, pulping, carrying out enzymolysis treatment, adding all the components, uniformly mixing, homogenizing, degassing while heating, canning, sealing, and sterilizing to obtain the finished functional papaya compound beverage product. The functional papaya compound beverage is rich in nutrient, and contains abundant proteins, amino acid, vitamins and multiple trace elements as well as multiple pharmaceutical components such as saponin, chlorogenic acid, oleanolic acid and the like. Besides, the functional papaya compound beverage product is vivid in color, rich in nutrient and sweet in taste, and can clear away heat and toxic materials, promote blood circulation, beautify face, protect liver, improve eyesight, resist bacteria, diminish inflammation, regulate intestine and stomach and improve human immunity, thereby having favorable health care effects.