Biological community structures have long been used to assess the impact of human activity on running waters. Although there were several studies using macroinvertebrate to assess the river conditions, the influence of hydrological factors, e.g. rate of flow, on community structure of macroinvertebrate and river health received little attention. In the present work, we investigated the community structure of macroinvertebrate and characteristics of environmental factors among 45 sampling sites in the Wei River Basin, Northwest China during wet season (October, 2011) and dry season (April, 2012). We also assessed the stream conditions of Wei River in the wet and dry seasons based on the Index of Biological Integrity (B-IBI). The results indicated that there was great heterogeneity in the structure of macroinvertebrate community in Wei River. The common species were Baetis vaillanti, Serratella sp., Leptophlebia sp., Cinygma sp., Pteronarcyidae, Hydropsychidae, Glossosomatidae, Cricotopus trifasciatus, Alotanypus venustus, Chironomus semireductus, Radix swinhoei, Radix ovata and Polypylis hemisphaerula. The structure of macroinvertebrate community in dry season is simplified. The results of boxing analysis showed that species richness, biomass and Shannon index were significantly higher in wet season than in dry season in the Wei River basin. However, the density of macroinvertebrate was similar in both seasons. The results of B-IBI showed that upstream of Wei River was of excellent ecological integrity, while the midstream and downstream of Wei River were in severe impairment. Though the biological integrity of macroinvertebrates in Jing River and downstream of Luo River was in severe impairment, the upstream of Luo River was in relatively good biological integrity. The score of B-IBI all over the Wei River basins showed positive correlations between wet and dry season. In this paper, we also discussed the influence of water flow and flux on the dynamic characteristics of macroinvertebrate community in wet and dry season. Moreover, the possible reasons that caused the difference in biological integrity of macroinvertebrate community in the Wei River Basin were further discussed.