The invention discloses a multi-use functional fertilizer and a preparation method thereof, and belongs to the technical field of fertilizers, and the multi-use functional fertilizer can be used for solving the problems of short fertilizer effect, single fertilizer effect, single function and easiness in causing land hardening and desertification. The fertilizer is prepared by fermenting nitrogen phosphorus and potassium, Chinese herbal medicine ingredients, sophocarpidine, humic acid, medium trace elements, biological bacteria and polypeptides, wherein the medium trace elements are calcium, magnesium, sulfur and silicon as well as iron, boron, manganese and zinc, and have the same amount; the Chinese herbal medicine ingredients are platycodon grandiflorum, lycoris radiate, nerium indicum, equisetum arvense, equisetum ramosissimum, elderberries, ailanthuses, xanthium sibiricum and polygonatum sibiricum. According to the fertilizer, the phenomena of soil hardening, deterioration, dysbacteriosis and the like caused by multi-year application of chemical fertilizers can be reduced and the root nutrient adsorption, transportation, storage and conversion capability is facilitated; after the fertilizer is applied, the yield of vegetables and the like can be increased by 20%-30%, the yield of fruit trees can be increased by 10%-20%, and the yield of economic crops such as peanuts and cotton can be increased by 10%-15%.