The invention relates to a breeding method of a beneficial microbe strain, comprising the following steps: preparing the culture medium solution of the beneficial microbe strain; diluting beneficial microbe strain bacterial solution containing the beneficial microbe strain with water; adding the culture medium solution in a container containing the diluted beneficial microbe strain bacterial solution; under the culture condition with the temperature of 10-40 DEG C and illumination, obtaining a beneficial microbe stock solution, namely obtaining a new beneficial microbe strain. The bred beneficial microbe strain in the method has the advantages of pure color and flavor and large content of strains in unit area. The large-scale container type producing method with open-air breeding is adopted and has the producing advantages of short time, fast breeding, wide spread culture condition and high yield of bacterial solution. The beneficial microbe bacterial solution bred by the method has the advantages of stable and reliable quality and simple and easy process, and can be widely applied to water treatment, aquaculture, feed adding, crop cultivation, fermentation of organic fertilizers, and the like.