The invention discloses novel multi-strain co-immobilized fermented papaya vinegar and a preparation method thereof. The preparation method comprises the steps of papayas selection, cleaning, blanching, peeling, seed removal, cutting, pulping, enzymolysis, centrifugation, component adjustment, pasteurization, cooling, co-immobilized alcohol fermentation, immobilized acetic bacteria fermentation, clarification, filtration, sterilization, ultrafiltration membrane purification, filling and product finishing. According to the novel multi-strain co-immobilized fermented papaya vinegar and the preparation method thereof, the problems that multiple papayas in the mature season are difficult to store, the traditional fruit vinegar fermentation is complicated to operate and the strains are liable to be deactivated can be solved effectively; the papayas can be used for batched fruit vinegar production, the production cycle is reduced and the production capacity is improved; the prepared papaya vinegar is clear and transparent, has stable color, is orange-yellow, has the prominent fragrance of the papayas, is faint scent, has mellow taste and soft mouthfeel, is good for a human body to digest and absorb food, and has the characteristics of invigorating spleen to promote digestion, prolonging life and the like.