The Western Route of the South-to-North Water Transfers Project represents a vital strategic initiative aiming at alleviating water scarcity in the Yellow River basin and northern China. Despite being in the planning and evaluation phase, establishing ecologically sustainable flow targets for rivers in the water source area remains a critical and challenging aspect of water diversion planning. In recent years, researchers have utilized the sensitive responses of benthic macroinvertebrates to hydrological conditions as indicators for determining ecological flow targets. However, there has been limited investigation into benthic macroinvertebrates in the water source area of the Western Route Project, with only a few studies conducted in distant locations such as the Yalong River and Dadu River, far from the proposed dam sites. To address this gap and explore the community structure of benthic macroinvertebrates while identifying suitable hydrological conditions in this region, two extensive surveys were conducted during both flood and non-flood seasons in 2022. Variations in benthic macroinvertebrate biological indices under different flow rates and water depths was analyzed using one-way analysis of variance and canonical correspondence analysis. Additionally, the research assessed the relationships between dominant benthic macroinvertebrate species and hydrological factors, determining optimal hydrological conditions and suitable ranges for dominant species using weighted averaging. Significant differences between optimal values and mean values of habitat factors were determined through a two-tailed t-test, while habitat suitability curves for dominant species were constructed using habitat simulation methods. The results revealed the presence of 50 genera of benthic macroinvertebrates in the two surveys, with the class Insecta dominating the community, constituting 90.20% of the total taxon. The dominant species varied temporally, with Heptageniidae sp. dominating during the flood season （ Y =19.9%）, and Perlidae sp. dominating during the non-flood season （ Y =13.8%）. Temporally, higher biological density was observed during the flood season, while higher biodiversity and species evenness were noted during the non-flood season. Spatially, biodiversity and biological density were significantly higher in the upper-route of the diversion project compared to the lower-route. Significant differences in species richness and the Margalef diversity index were observed among different velocity intervals within the 0-1.0 m/s range, with the highest number of species and various biodiversity indices found in the 0.5 to 1.0 m/s range during both flood and non-flood periods. Similarly, significant differences in biomass were observed between different depth intervals within the 0-0.6 m range, with the highest benthic macroinvertebrate density recorded in the 0-0.2 m interval. Targeting seven dominant species in the water source area, suitable hydrological conditions were determined to be a water depth of 0.2-0.4 m and flow velocity of 0.3-0.6 m/s using habitat suitability simulation methods. In conclusion, during the survey period, 50 genera of benthic macroinvertebrates were recorded in the water source area of the Western Route Project, with Insecta being the dominant group, particularly Heptageniidae sp . during the flood season and Perlidae sp. during the non-flood season. Temporally, higher biological diversity and species evenness were observed during the non-flood season, emphasizing the importance of ecological base flow protection during this period to maintain river biodiversity. Spatially, benthic biological diversity and density were higher in the upper scheme water diversion sections compared to the lower scheme water diversion sections. The recommended suitable ranges for water depth and flow velocity for dominant species of large benthic animals in the water source area rivers were determined to be 0.2-0.4 m and 0.3-0.6 m/s, respectively. These findings can contribute valuable insights for simulating and evaluating suitable habitats for benthic animals in the water source area of the Western Route Project.