The invention discloses a composite micro-ecological bacterial agent for improving eutrophication of a water body and a preparation method thereof, and belongs to the technical field of microbial fermentation. The composite micro-ecological bacterial agent comprises bacillus subtilis, bacillus megatherium, bacillus aryabhattai, thiobacillus and respectively corresponding bacillus and thiobacillus carrier culture media. According to the composite micro-ecological bacterial agent for reducing eutrophication of the water body, which is provided by the invention, the main research and development direction is to reduce ammonia nitrogen, hydrogen sulfide and organophosphorus in the aquaculture water body and maintain proper water quality, different strain production and drying processes are reasonably prepared, and metabolic characteristics of the bacillus subtilis, the bacillus megatherium, the bacillus aryabhattai and the thiobacillus are integrated, so that the bacillus subtilis, the bacillus megatherium, the bacillus aryabhattai and the thiobacillus can take a synergistic effect, the aims of reducing excessive enrichment of ammonia, nitrogen, sulfur and phosphorus and reducing the risk of environmental pollution are fulfilled, the proper water quality is maintained, and the environmental pollution is reduced.