The invention discloses a medlar and red date enzyme and a preparation method thereof, which belong to the technical field of enzyme preparation. Multi-strain composite fungi powder is adopted as a leavening agent; the medlar and the red date are adopted as main raw materials; dietary fiber, pectin hydrolyzate, seasoner extracting liquor, Chinese herbal medicine extracting liquor, enzyme stabilizer and other multifunctional auxiliary raw materials are scientifically compounded and modified; low-temperature processing technology such as ultrasonic cleaning, cryogenic grinding, microwave-assisted high-voltage pulse electric field processing and ultrasonic ripening are mainly adopted in the whole process, so that the natural colors, the flavor, the taste and the content of the active materials of the medlar and the red date are maintained furthest, the biological stability, the non-biological stability and the biological activity of the medlar and red date enzyme are obviously enhanced, the introduction of chemical addition agent is reduced, and the juicing rate of the medlar and the red date as well as the food safety of the enzyme are improved. Finally, the medlar and red date enzyme with high biological activity, strong stability, strong taste, flavor and appetite, long expiration date and edible safety is prepared.