The invention discloses a preparation method of environment-friendly shallow sea fish compound feed. The preparation method comprises the following steps: grinding fermented soybean meal for later use; mixing and grinding rhubarb, safflowers, atractylodes macrocephala, eucommia bark leaf powder, pericarpium citri reticulatae and garlic, boiling the mixed powder with hard fire, decocting the mixed powder with soft fire, carrying out filtration three times, mixing the filtrates, and decocting the mixed filtrate into a thick shape so as to obtain a compound immunopotentiator; and taking the fermented soybean meal powder and the compound immunopotentiator, adding and uniformly mixing dephenolized cottonseed protein, soybean protein, fish dissolved pulp protein, wheat meal, flour, phospholipid oil, vitamin complex, oyster powder, artemia powder, a food attractant, yeast powder and crab spawn powder, and then, carrying out hardening and tempering, puffing, granulating, baking and cooling to obtain the environment-friendly shallow sea fish compound feed. The preparation process is simple, the utilization ratio of the raw materials is high, the loss of nutritional ingredients in the preparation process is less, and the prepared feed has a reasonable nutrition structure, is suitable for breeding of shallow sea fishes in the young stage, growth stage and adult stage, is environment-friendly and is free of pollution to the environment.