The invention discloses a preparation method of traditional Chinese medicine composition for purifying mandarin fish ponds. The method comprises steps as follows: baical skullcap roots, black nightshade herbs, fresh ginger, pomegranate rinds, red peony roots, cyrtomium rhizomes, perilla stems, peonies, arnebia roots, liquorice roots, argy wormwood leaves, stemona roots, acanthopanax root bark, tobacco leaves, pepper and ageratum are crushed, screened through a sieve of 60-70 meshes, soaked in water, heated and cooked until the moisture content is 20wt%-45wt%, hydroxyethyl cellulose is added, the mixture is stirred and granulated, and first preformed materials are obtained; alkaloid, Celastrus angulatus, Artemisia toosendanin, orange terpenes, pyrethrins and poly(aspartic acid) are evenly stirred, stir-fried shells, illite, illite smectite clay, diethylene glycol butyl acetate and microcrystalline wax are added and stirred, the mixture is atomized and sprayed onto surfaces of the first preformed materials, and second preformed materials are obtained; Celastrus angulatus missible oil, sodium carboxymethylcellulose, nacre mothers of pearls, activated carbon, an EM (effective microorganisms) liquid and water are evenly mixed, the mixture is atomized and sprayed onto surfaces of the second preformed materials, the second preformed materials are dried and screened, and the traditional Chinese medicine composition for purifying the mandarin fish ponds is obtained.