As the largest tributary of the Yangtze River and a core area of the Middle Route of the South-to-North Water Diversion Project, the Han River Basin holds significant ecological importance regarding the impacts of land use and water environment changes on aquatic ecosystems. Existing studies have mostly focused on local reaches of the upper or middle–lower Han River, and systematic investigations into the associations between macroinvertebrate communities and environmental factors at the entire basin scale remain scarce. The niche characteristics and environmental drivers of macroinvertebrate community structure in the Han River Basin, China, were evaluated using a variety of diversity metrics and statistical methods. The results showed that: (1) A total of 91 macroinvertebrate taxa were identified during 2022–2023, with Insecta as the dominant group. Species richness in the upstream reaches increased in 2023, and the degree of differentiation between the upstream and the middle–lower reaches was markedly weaker than that in 2022. (2) Significant interannual differences in macroinvertebrate community structure were detected (PERMANOVA, p < 0.05), and taxa such as Polypedilum sp., Orthocladius sp., and Gammaridae collectively accounted for 35.6% of the dissimilarity among communities. (3) The overall niche breadth of dominant taxa was relatively low, whereas niche overlap decreased significantly in 2023, indicating a community niche pattern characterized by “low competition–high differentiation”. (4) Total phosphorus (TP) and total nitrogen (TN) were the core water environmental factors driving changes in community structure, while forested land was the key land use factor, and their synergistic effects jointly regulated the composition and diversity of macroinvertebrate communities.