The invention provides a preparation method of a root fertilizer for preventing and treating diseases and pests attacking curcuma zedoary. The preparation method comprises the following steps: (1) weighing 30-50 parts by weight of Chinese mesona herb residues, 20-40 parts by weight of sheep manure, 15-20 parts by weight of peanut bran, 5-10 parts by weight of molasses, 5-10 parts by weight of marigold, 10-15 parts by weight of coffee grounds, 3-8 parts by weight of Derris trifoliata, 3-8 parts by weight of Polygonum hydropiper and 5-8 parts by weight of borax; (2) separately crushing the marigold, coffee grounds, Derris trifoliata, Polygonum hydropiper and borax, separately carrying out sieving with a sieve with a size of more than 40 meshes, and putting the sieved materials aside for later use; (3) adding the sheep manure and EM bacteria into the Chinese mesona herb residues, carrying out mixing, stacking and fermenting for more than one month until the Chinese mesona herb residues are completely melted into loose powder so as to obtain a decomposed material; (4) uniformly mixing the decomposed material with the peanut bran, molasses, marigold, coffee grounds, Derris trifoliata, Polygonum hydropiper and borax powder, adding a proper amount of water until the materials are wet, and carrying out hermetical stacking for 3-5 days; and (5) granulating the stacked materials by usinga drum granulation method so as to obtain granules, spraying a layer of alcohol waste liquid on the outer layer of each granule, and carrying out drying, sealing and packaging to obtain a product. The product prepared by using the method not only can be used as a root fertilizer for curcuma zedoary, but also can prevent and treat the root rot disease of curcuma zedoary.