Identifying naturally-regulated spatial and temporal variations of benthic macroinvertebrates is critical for effective assessment and conservation of aquatic ecosystems. A clear identification of spatial and temporal trends of these communities could enhance our understanding of the ecology of macroinvertebrates, definitions of effects of anthropogenic or natural disturbances on lotic communities, and assessment and conservation of lotic biodiversity. In the present study, macroinvertebrate community structure was compared among different seasons in the upper Newxue River in the year 2012 (April, October, and December), where a total of 108 macroinvertebrate taxa belonging to 74 genera and 10 classes were recorded; Cheumatopsyche sp., Orthocladius vaillanti, Paratanytarsus sp., and Neozarelia sp. were the dominant taxa, with relative abundances of 25.1%, 9.8%, 9.0%, and 8.6%, respectively. Dominant species composition was very different across seasons; Cheumatopsyche sp. was the only common taxon in all three seasons. Density, species richness, and Shannon index were significantly higher in April and December than in October; evenness was highest in October. Non-metric Multidimentional Scaling (NMS) analysis was used to compare the community structure among different seasons in the Newxue River and typical reaches, and the results all showed significant differences; seasonal differences in the control reach (reach D) were relatively small. A total of 41 representative species of the Newxue River and typical habitats were separated by indicator species analysis, but no species was isolated from reach B. Two-way cluster analysis further clarified the indicator attributes (unique or highest relative abundance) of the indicator species.