The impact of hyporheic exchange on the community structure of macroinvertebrates is a crucial topic in current river ecosystem health research. As a primary tributary of the Yellow River, the ecological status of the Weihe River Basin serves as a critical indicator of the overall health of the Yellow River ecosystem. In this study, we focus on the Weihe River Basin to explore the effects of hyporheic exchange intensity and different degrees of heavy metals pollution on the structure of macroinvertebrate communities. Macroinvertebrate and sediment samples were collected from 12 sites along the mainstream Wei River, Jing River, and Beiluo River from October to November 2023. The falling-head permeameter test method was employed to measure the hydraulic conductivity and hyporheic exchange flux, while sediment heavy metal content, particle size distribution, and macroinvertebrate information were also determined. The research has 3 major findings: ①a total of 277 macroinvertebrates, belonging to 3 phylums, 4 class, 8 orders, 15 families, 18 genera and 20 species, were collected from the 12 sampling sites, among which arthropods were the most abundant, followed by mollusks. The highest average density was found in the Tanytarsus, while the highest biomass was found in the Bellamya purificata. Based on the Biological Pollution Index (BPI) classification criteria, the sediments at each monitoring site are generally at light to moderate pollution levels, while based on the Family Biotic Index (FPI) classification criteria, the sediments at each monitoring site are generally at clean levels; ②the comprehensive pollution status of the study area was at a light to moderate pollution level, with relatively severe As pollution. Heavy metals (Zn, Pb) were positively correlated with the richness of macroinvertebrates; ③the vertical hydraulic conductivity(K_v) of the hyporheic zone varied between 0.23 and 3.50 (m/d), showing significant differences in different rivers. Hyporheic water exchange is mainaly downwelling. The research findings provide theoretical support for understanding the maintenance of aquatic ecosystem health in the Yellow River Basin. They also offer a scientific basis for ecological protection and high-quality development in the region.