The Wuding River Basin is located in the transition zone between the Loess Plateau and the Mu Us Sandy Land, characterized by extensive soil erosion and a fragile and volatile ecological environment. In this study, water ecosystem surveys were conducted in the spring (April) and autumn (October) of 2021 in the upper, middle, and lower reaches of the Wuding River Basin, its six tributaries, and three check dams in the basin, to map the characteristics of the benthic community in the Wuding River Basin, constructing the benthic integrated biotic index of Wuding River and conducting health evaluation. A total of 105 species of benthic macroinvertebrates with an average density of 181 ind./m² and an average biomass of 0.760 g/m² were collected in the Wuding River Basin in spring, and 67 species of benthic macroinvertebrates with an average density of 94 ind./m² and an average biomass of 0.454 g/m² were collected in autumn. By carrying out distribution range test, discriminatory ability analysis and correlation analysis for 27 biological parameters of benthic macroinvertebrates in the study area in two seasons, we constructed the benthic integrated biotic index(B-IBI) of the Wuding River Basin, and carried out the B-IBI health evaluation for 40 sample sites (6 reference sites and 34 impaired sites) in the whole basin. The evaluation results showed that, in general, the benthic biotic integrity of the Wuding River Basin was good, with 19 of the 40 sampling sites in a healthy or sub-healthy state in spring and 23 in a healthy or sub-healthy state in autumn, of which the upper and middle reaches of the Wuding River were mostly healthy and sub-healthy, while the lower reaches of the Wuding River and the three check dams were in a poor state of health. There were significant differences in the characteristics of benthic communities and biological integrity evaluation in different soil erosion areas. The results of this study can provide a scientific basis for assessing the ecological health of the Wuding River Basin.