The invention discloses a substrate for preventing and treating soil diseases and pests and apreparation method thereof. Zhibaidihuang pill residues and sanhuang tablet residues serve as raw materials; the residues are dried, crushed and mixed; by volume, water which is 6-10 times of the residue is added to the residue; cellulose and pectinase are added to perform enzymolysis, and inactivation is performed at 100 DEG C; activated enzyme microorganism is added to perform maturity and fermentation, and the residues are dried to obtain the substrate. The traditional Chinese medicine residues are utilized to undergo fermentation to produce the substrate, the waste is turned into wealth, and the substrate can be used for vegetables, fruit trees, flowers and other crops to perform field prevention and treatment of soil diseases and pests. The substrate not only can inhibit soil diseases and pests, obviously reduce diseases and pests on the ground and protect beneficial microorganisms, but also can provide soil nitrogen, phosphorus and potassium and improve plant immunity.