Abstract: In order to solve the soil problems caused by excessive application of chemical fertilizer in the process of soybean planting, and evaluate the impact of microbial bacterial fertilizer on soybean rhizosphere fungal community from fungal diversity and composition structure, this study studied the changes of fungal diversity and structural composition in soybean rhizosphere soil at flowering stage by reducing the application of chemical fertilizer and microbial bacterial fertilizer. The results showed that Ascomycota, Mortierellomycota and Basidiomycota were the main flora, and Ascomycota was the main dominant flora. There were differences in rhizosphere fungal communities in the same plot with different fertilization methods. Reducing chemical fertilizer combined with microbial compound bacterial fertilizer can effectively reduce the abundance of Fusarium, and applying microbial bacterial fertilizer alone can effectively improve the abundance of Penicillium and aspergillaceae. In conclusion, microbial fertilizer can increase the abundance of beneficial bacteria and reduce the abundance of pathogenic bacteria.