The invention discloses special EM (Effective Microorganisms) bacteria powder for aquaculture, as well as a preparation method and application of the special EM (Effective Microorganisms) bacteria powder. Bran, corn flour, amino acid powder and the like, which are used as dry matter fillers, are mixed with brown sugar, glucose and the like to obtain a mixture; the mixture is subjected to sealing fermentation at 25-37 DEG C for about 10 days by lactic acid bacteria, bacillus licheniformis and bacillus coagulans, so that fermented materials are prepared; then the prepared fermented materials are dried and crushed and are mixed with bacillus subtilis to obtain a final product. The EM bacteria powder can be directly scattered in a water body to inhibit pathogenic microorganisms through mass propagation of probiotics, decompose harmful substances in the water body, promote the growth of normal floras and beneficial algae in a cultivation ecosystem and keep the ecological balance of the aquaculture water body. The method is adopted to prepare the EM bacteria powder, the fermentation period is short, the process is simple, the equipment investment is low, the materials are convenient to obtain, and the method is easy to implement and is suitable for industrial production and self-production of households.