It is of great significance to study the community structure of macrobenthos and the water quality for protection and restoration of aquatic ecology. Taking the Qingyi River Basin as the research object, a survey of macrobenthos and physicochemical factors of the water body was carried out in September 2020. It analysed the structural characteristics of the macrobenthic community by means of the relative importance index, the biodiversity index and the Jaccard similarity coefficient. It investigated the extent of disturbance to the benthic community and the main environmental factors that affect it, by applying the comparative abundance/biomass curve method and redundancy analysis. Finally, the comprehensive index of water ecological environment quality was used to evaluate the river water quality. The results showed that (1) 61 species of macrobenthos were collected and identified in the Basin, which belonged to 3 phyla, 6 classes and 17 orders. The average density was 265.9 ind/m² while the average biomass was 41.6 g/m². The main dominant species which were shown in the index of relative importance in the community were Macrobrachium nipponensis, Cipangopaludina chinensis, Chironomus plumosus, and Ecdyrus. (2) The Jaccard similarity coefficient was low due to the analysis of community similarity, with a strong spatial heterogeneity between the investigation sites. (3) The main environmental factors-conductivity, ammonia nitrogen concentration and flow velocity-influenced the community structure of macrobenthos by the redundancy analysis. (4) The biological index analysis results indicated that the water quality in the basin was lightly or moderately polluted, which varied significantly from the assessment of the physical and chemical factors of water quality. The comprehensive water and ecological quality index model calculations, which integrated biotic and abiotic factors, suggested an overall water and environmental quality preference for the basin. But some sampling points have been disturbed or polluted, which was basically consistent with the abundance-biomass comparison curves analysis and the dominant species analysis, in which the result of evaluation was more scientific and reliable.