Understanding community spatio-temporal variability is the basis for further research (such as trait, functional diversity, and so on). Most studies to date have focused on the relationship between community structure and environmental factors, and species composition has been only rarely reported. In the present study, macroinvertebrate community structure was compared among typical stream habitats in the upper Newxue River in the year 2012 (April, October, and December). The main results were as follows:a total of 108 macroinvertebrates taxa belonging to 74 genera and 10 Classes were recorded; Cheumatopsyche sp., Orthocladius vaillanti,Paratanytarsus sp.E, and Neozarelia sp. were the dominant taxa, with relative abundances of 25.1%, 9.8%, 9.0%, and 8.6%, respectively. Dominant taxon composition, density, biomass, ratio of biomass and density, and biodiversity indices (richness, Shannon index, and evenness index) were significantly different among different reaches. Non-metric multidimensional scaling (NMS) and multiple response permutation procedure (MRPP) showed that community structure was significantly different among the reaches, and this difference increased with decrease in flow rate. Indicator species analysis and two-way cluster analysis were used to explain the reasons for differences in community structure at the species level. The protection of habitat diversity is thus of great significance for the protection and improvement of biodiversity in the study area.