The invention relates to a Chinese herbal medicine compound bait, as well as a preparation method and application of the Chinese herbal medicine compound bait. The Chinese herbal medicine compound bait comprises the following Chinese herbal medicine components by weight percent: 20-30% of radix pseudostellariae, 5-10% of cordyceps sinensis, 10-15% of lycium chinense, 10-15% of clove, 10-15% of honeysuckle, 10-15% of radix bupleuri, 5-10% of liquorice, 5-10% of radix astragali, 1-5% of poria cocos and 1-5% of borneol; and the Chinese herbal medicine compound bait comprises the following basic bait components by weight percent: 30-35% of sea mud, 10-15% of kelp meal, 4-6% of shell powder, 10-15% of sargassum thunbergii powder, 0.5-1% of spiral seaweed, 3-5% of fish meal, 3-5% of vegetable protein, 1-3% of shrimp meal, 2-3% of scallop skirt, 0.6-0.8% of yeast tablets, 2-2.2% of composite mineral salt and 1.8-2% of multivitamin. The Chinese herbal medicine components are mixed into the basic bait components according to the ratio of 2-5%, and the mixture has the particle size of 250-300 meshes. The Chinese herbal medicine compound bait provided by the invention is capable of obviously increasing the weight gain rate and survival rate of stichopus japonicus, reducing the splanchnic ratio, and improving the immunity of the stichopus japonicus; and the Chinese herbal medicine compound bait is free from toxic and side effects, can be used for remarkably improving the 'skin ulceration syndrome' resistance of the stichopus japonicus and has the advantages of reducing the food coefficient as well as NH3-N content and chemical oxygen demand (COD) content in aquaculture water, and the like, thus having good guiding significance for increasing the yield of stichopus japonicus aquaculture and the prevention and treatment of diseases.