The invention provides a preparation method of a fermented traditional Chinese medicine for preventing and treating intestinal diseases of aquatic products. The fermented traditional Chinese medicineis also called a bacterial medicine, water is added into a traditional Chinese medicine composition, compound fermentation strains are inoculated, and fermentation is performed to obtain the fermentedtraditional Chinese medicine. The invention further provides the corresponding fermented traditional Chinese medicine. The fermented traditional Chinese medicine has the functions of internally strengthening digestive absorption, nourishing stomach and protecting liver and externally resisting mushroom poisons and killing pathogens, and is used for preventing and treating the intestinal diseasesin aquaculture and applicable to prevention and treatment of the intestinal diseases of special aquaculture animals such as various saltwater fishes, freshwater fishes, shrimps, crabs, sea cucumbers,turbots, bastard halibuts, large yellow croakers, snappers, sea eels, globefishes, rice field eels, soft-shelled turtles and ictalurus punctatus. The fermented traditional Chinese medicine has good effects on the intestinal diseases such as white intestine diseases, empty stomach, white discharge and hangover caused by bacteria, viruses and antibiotics, and particularly has special effects on fatal diseases of the shrimps caused by enteritis, white discharge, empty intestines and empty stomach.