Understanding the drivers of macroinvertebrate community structure is fundamental for adequately controlling pollutants and managing ecosystems under global change. In this study, the abundance and diversity of benthic macroinvertebrates, as well as their chemical parameters, were investigated quarterly from August 2014 to April 2015 in four reaches of the Huai River basin (HRB). The self-organizing map (SOM) algorithm and canonical correspondence analysis (CCA) were simultaneously applied to identify the main factors structuring the benthic community. The results showed that the benthic community structure was always dominated by gastropoda and insecta over seasons and presented obvious spatial and temporal heterogeneity along different pollution levels. The insects were always the top contributors to number density of the benthic community, except for the summer, and the biomass was mainly characterized by mollusca in all seasons. Statistical analysis indicated that TN and NH₃-N in water, as well as Hg, As, Cd, and Zn in sediments, were the dominant factors structuring the community, which determined the importance of sediment heavy metal concentrations in explaining the benthic community composition in comparison with other factors. These major factors should be given priority in the process of river pollutant control, which might be rated as a promising way to scientifically improve river health management and ecological restoration.