Riffle and pool, which exhibit very different physical characteristics (such as depth, velocity, substrate), are basic and common habitat units in mountain rivers. The benthic macroinvertebrate is an important connector among the different trophic levels of stream ecosystem and its community could be easily affected by variation of physical characteristics of microhabitat. However, previous researches did not always demonstrate a clear difference of community structure and diversity between riffle and pool macroinvertebrate. Dong River is a typical mountain stream which is located in a karst area of southwestern China, namely Kaixian County of Chongqing. In order to study variations in structure, composition and diversity between riffle and pool macroinvertebrate assemblage, we chose twenty one pairs of riffles and pools to investigate benthic macroinvertebrate species in upstream of Dong River in July 2011. Our results indicated that the difference of water quality was not significant between the two habitats. However, the riffle habitat not only had a wider water surface and faster flow velocity, but also contained bigger substrate than those of the pool habitat. The number of species was thirty one in riffles and twenty four in pools. Density and wet biomass of macroinvertebrate assemblage in riffles were 450.62 ind/m² and 2.88 g/m², respectively, comparing to 86.24 ind/m² and 0.55 g/m² in pools. Mayfly was the group with the highest density, abundance and species richness in both habitats. Virtually all species were more abundant in riffles than those in pools, except chironomids, Ephemera sp and Hexatoma sp which were more abundant in pools. Indicator Species Analysis indicated that a greater number of taxa, including Hydropsyche sp, Iron sp, Pseudocloeon sp, Glossosoma sp, Epeorus sp2, Notacanthurus sp, Heterocloeon sp, Serratella sp, Antocha sp, Isonychia sp and Rhithrogena sp, were restricted to riffles, while only two species, Ephemera sp and Hexatoma sp, were indicator species of pools. Kruskal-Wallis Test indicated that relative abundance of each functional feeding group was significantly different between the two habitats. Scraper was the dominant functional feeding group in both habitats, while shredder had the lowest relative abundance. Relative abundance of functional feeding groups between riffle and pool were significantly different except that of shredder. Riffles exhibited significantly higher percentage of collector-filterer and scraper, while percentage of collector-gatherer and predator in pools were significantly higher than that of riffles. Detrended Correspondence Analysis indicated that the difference of macroinvertebrate community structure was obvious between the two habitats. Density, wet biomass, species richness, Shannon-Wiener index and Improved Shannon-Wiener index of riffles were significantly higher than those of pools, which was similar with former researches conducted in mountain stream with stony substrate. Pool characterized by small and loose substrate is unstable and vulnerable habitat for benthic macroinvertebrate to resist fast flow during the flooding period. However, bigger substrate of riffle as a result of erosion creates a much more diverse and stable for macroinvertebrate to escape predators and disturbance of scouring. Therefore, habitat stability and heterogeneity affected by habitat morphology, hydraulic characteristics and erosion/deposition pattern may be the major explanation.