The invention relates to a pesticide residue degradation agent for modern Chinese medicines and a preparation method thereof. A micro-nano biotechnology, an enzyme active substance control technology and the like are utilized for the produced pesticide residue degradation agent for the modern Chinese medicines. The plant cell membrane function can be improved by enzyme action and biological decomposition action after the agent is used; an intelligent, sustained and auxiliary agent is also added to improve and change the plant quality; pesticide and heavy metal residues are degraded; the traditional Chinese medicines are strengthened; and agricultural products can be facilitated to achieving the international standard. The pesticide residue degradation agent for the modern Chinese medicines, disclosed by the invention, is prepared from the following materials in parts by weight of: 300-350kg of a pig pancreas extract, 100-150kg of styrene acrylic amino acid concentrate, 50-100kg of plant humic acid, 30-70kg of bone glue, 20-50kg of boric acid, 50-100kg of smoke alkali liquor, 50-200kg of ethanol, 170-500kg of water, 5-10kg of vanillic aldehyde, 1-5kg of compound sodium nitrate powder liquid, 50-150kg of urea, 40-120kg of pyroligneous, 5-10kg of flavones, 5-10kg of ferrous sulfate, and 1-5kg of citric acid by using a certain preparation method.