The West Route of the South-to-North Water Transfer Project will divert water from the upper Yangtze River and its tributaries-the Dadu River and Yalong River- to the upper Yellow River. The project may ease the water shortage in the Yellow River Basin. However, the project may have some effects on the ecosystem in the upper Yangtze River Basin. The benthic invertebrates play an important role in the river ecosystem and act on the circulation of materials and nutrition. The benthic invertebrates are widely applied to quickly assess the river ecosystem for their rapid response to the change of the water environment. The diversity of the benthic invertebrates is closely associated with the aquatic habitat area. This paper works on the coupling interaction between them by sampling in the benthic invertebrates in an area of expanding. The conclusions are drawn that the diversity of the benthic invertebrates will begin to decrease when the habitat area is reduced to 45% of the original area, and decrease greatly when the habitat area is reduce to 10%. The aquatic habitat area shall be kept more than 45% of the original area in order to maintain the high diversity of the benthic invertebrates. Keywords: West Route Project; River ecosystem; Benthic invertebrates; Biodiversity; Aquatic habitat area