Benthic macroinvertebrates are widely used as bioindicators for assessing freshwater ecosystem health. This study investigated the diversity patterns and community structure of benthic macroinvertebrates across 21 sampling sites along the middle and lower reaches of the Yangtze River. A total of 74 species belonging to 3 phyla, 7 classes, 17 orders, 37 families, and 58 genera were identified, with aquatic insects dominating the assemblages. Alpha diversity indices showed no significant differences among river sections, whereas multivariate analyses (NMDS and PERMANOVA) revealed significant spatial variation in community composition, indicating that beta diversity plays a key role in structuring assemblages at the basin scale. Canonical correspondence analysis (CCA) identified nutrient variables (TN and NH₄⁺-N), as well as pH and conductivity, as the main environmental drivers influencing community distribution. The results suggest that benthic macroinvertebrate diversity patterns in large river systems are jointly shaped by regional environmental gradients and local habitat conditions. These findings provide insights into biodiversity conservation and ecological management of large river ecosystems.