The Yellow River Delta region has a wide range of natural resources and significant ecological conservation value, but the presence of multiple pollution sources during urbanization and industrialization has resulted in complex pollution. The change of salinity gradient in the water bodies of the Yellow River Delta basin has further led to an increasingly complex status of composite pollution in the water bodies of the Yellow River Delta basin. In this paper, Cu²⁺ and aniline were selected as the target pollutants and response surface experiments were conducted under different salinities and different pollutants in the water bodies of the Yellow River Delta watershed as the medium to analyze the changes of microbial flora under different factors; the composition structure and dominant strains of microbial flora in the water bodies of the Yellow River Delta in the presence of Cu²⁺ and aniline separately and in the presence of both pollutants together were analyzed by high-throughput sequencing; the analysis of The changes in the diversity of each group under different pollution conditions and the differences between groups were analyzed. The aim was to reveal the influence of pollutants on the diversity and structural composition of microbial communities in the presence of complex pollution.