Small hydropower plants diverted water and deteriorated river ecosystem and aquatic biodiversity. The release of ecological flow is an important measure to restore the damaged ecosystem of diverted rivers. Benthic macroinvertebrate are commonly used indicator organisms for aquatic ecosystem condition and restoration as they are sensitive to environmental variation. In 2021, the discharged flow, physical habitat, water quality and benthic macroinvertebrate of riffle habitat immediately below ecological flow outlets (evaluated site) of eight typical small hydropower plants (SHP), which located at the Yipin River and the Wubu River in Banan District, Chongqing, were investigated and compared with near natural reaches (reference site). We aimed to evaluate the ecological effect of flow discharge and discover the ecological mechanism of benthic macroinvertebrate restoration. The results indicated that the only one SHP's discharge could completely reach designed ecological flow value. The average achievement rate of non-compliant ecological flow release was 41.0%. Channel wetted rate of the evaluated sites was 47.6% at average. There was no significant difference in water quality between evaluated and reference sites. Aquatic insect biomass and richness at most evaluated sites and benthic macroinvertebrate density at all evaluated sites were significantly lower than those at reference sites. Those three indicators at evaluated sites were 24.5%, 43.2% and 25.8% of that at reference sites, respectively. There were no significant differences in Shannon-Wiener diversity and Pielou index between evaluated and reference sites. Benthic macroinvertebrate community compositions at both evaluated and reference sites were similar and dominated by EPT insets (Ephemeroptera, Plecoptera and Trichoptera). The dominated functional feeding groups of evaluated sites were collector-gatherer and scraper, which was similar to reference sites, but densities of each functional feeding group were significantly lower than that at reference sites. Density, richness and EPT inset density at evaluated sites were positively correlated linearly with channel wetted rate. Insufficient discharge and reduced organic debris input limited restoration of benthic macroinvertebrate. Present study indicated that there were no significant differences in water quality, benthic macroinvertebrate community diversity, community structure, and functional feeding groups between riffle habitat immediately below SHP dam and in near natural reaches as a result of ecological flow release. Benthic macroinvertebrate density, aquatic insect biomass and richness, and EPT inset density in former didn't recover well enough. The restoration of ecosystem in diverted reaches after ecological flow release has not yet met expectations. Insufficient flow release was found to be a major determinant in benthic macroinvertebrate community recovery.