The invention discloses a traditional Chinese medicine preparation for treating bacterial intestinal hemorrhagic diseases of small water turtles and a preparation method thereof, aims to solve the problems of high death rate, high breeding risk and low economic benefit caused by bacterial intestinal hemorrhagic diseases of small water turtles, and belongs to the technical field of processing of feed additives of turtles. The traditional Chinese medicine preparation comprises the following raw materials: rheum officinale, radix astragali, cortex phellodendri, radix scutellariae, coptis chinensis, andrographis paniculata, dark plum, fructus chebulae, platycodon grandiflorum, caulis perllae, radix achyranthis bidentatae, dandelion, garden burnet, radix isatidis, cordate houttuynia, cayratia japonica, chenopodium ambrosioides, phyllanthus urinaria, bighead atractylodes rhizome and acalypha australis. The traditional Chinese medicine preparation is prepared by drying, crushing, screening, mixing and sterilizing. The traditional Chinese medicine preparation integrates functions of various traditional Chinese medicines, has antisepsis and anti-inflammation effects, can be used for effectively treating the bacterial intestinal hemorrhagic diseases of the small water turtles, is sterilized at high temperatures under high pressure, is short in time, excellent in effect, long in preservation time, simple in operation of preparation method and low in production cost, and is suitable for popularization and application.