Aquaculture often has scale incidence prevalence, and the common problem most closely related to incidence is aquaculture water environmental degradation. The invention relates to a method for preparing a protective material for reducing the ammonia-nitrogen level of aquaculture water and application of the protective material. According to the method, endspores and denitrified microbial flora in a pond water body and bottom sediment in a specific culture region are subjected to enrichment culture, and are added into a solid culture material to prepare the endspores and aerobic denitrifying flora-enriched microbial culture material by means of solid fermentation. Simulation tests indicate that the protective material used in a specific culture region can effectively reduce the ammonia-nitrogen level of the culture water body, maintain the stability of water quality in the culturing process and remarkably reduce the incidence rate. The method has simple operation and low cost, and can be applied to culture regions in large scale efficiently and accurately.