The invention discloses a method for cooperative control of microcystis aeruginosa by using chub, bighead, silver xenocypris fish and daphnia magna, and belongs to the technical field of water treatment. The microcystis aeruginosa in water is controlled through a food chain relationship; the chub, the bighead, the silver xenocypris fish and the daphnia magna can directly eat the microcystis aeruginosa in a filtering manner; meanwhile, the chub, the bighead and the silver xenocypris fish also can intake the daphnia magna, so as to indirectly consume the microcystis aeruginosa in water; the fish, the daphnia magna and the microcystis aeruginosa form the food chain relationship. In addition, the upper, middle and lower microcystis aeruginosa and a microcystis aeruginosa resting body at the bottom can be controlled by fully utilizing the vertical spatial distribution difference of the three fishes in the water, the content of the microcystis aeruginosa in the water can be more effectively controlled, the eutrophication level is reduced, the balance of an ecological system of the water is facilitated, and meanwhile, certain economic value can be obtained by catching the chub, the bighead, the silver xenocypris fish. The method has the advantages of low cost, no secondary pollution and the like, and is simple and feasible.