The stream hyporheic zone is an ecotone of surface water-ground water interactions, is rich in biodiversity, and is an important component of stream ecosystems. The hyporheic microinvertebrates inhabiting the hyporheic zone directly influence the matter and energy dynamics of the hyporheic zone, are potential indicators of the ecological health of the river, adjust the functions of environment purification and ecological buffering, and play an important role in the structure and function of stream ecosystems. The composition and distribution of the hyporheic macroinvertebrates are affected by natural factors and human activities. The recolonization processes of hyporheic microinvertebrate communities were studied using artificial substrates in a mountain stream. Our results indicate that the individual density of microinvertebrates showed the J type growth curve from 7 to 29 days, declined suddenly after 29 days, and showed a fluctuating trend after 55 days. The trend of decline after 29 days was not only influenced by environmental capacity and interspecific competition, but also by external environment factors. During this period, sustained rainfall caused floods in the study area. The richness of macroinvertebrates showed an increasing trend from 1 to 29 days and a fluctuating trend after 29 days. The biomass of macroinvertebrates generally showed an increasing trend. The richness, density, and biomass of macroinvertebrate communities showed no significant difference at 29, 71, and 83 days (P > 0.05). The Shannon-Wiener and Pielou indices also showed no significant difference at 55, 71, and 83 days (P > 0.05). The species density before and after disturbance was used to indicate the recovery state of the community. However, in the long time scale, using only species density did not accurately reveal the recovery state of the stream ecosystem, because of the influence of environmental factors and life history strategy. According to the comprehensive analysis based on these trends and the principal component analysis of species abundance in different recolonization time, macroinvertebrate communities of the hyporheic zone tend to stabilize after 55 days. The dominant species were Camptochironomus sp., Corbicula fluminea, Baetis sp., Cinygmina sp., Hydropsyche sp. and a member of the Psephenidae. In all 28 species macroinvertebrates, 20 species were aquatic insects, which comprised the dominant assemblage of macroinvertebrates. Collector-filterers and collector-gatherers were the dominant functional feeding groups during the whole process. The recolonization of hyporheic microinvertebrate communities is an interactive process of its own resilience and external environment factors. The resilience of communities was determined by the life history strategy, adaptability, and interspecific and intraspecific interactions of species. The external environment factors include the environmental capacity, drought, and flood. In the initial stage of recolonization, the most important factor was the structure of hyporheic zone that controlled macroinvertebrate moving into the habitat, the life history strategy was the most important factor in the interim period, and in the stable period, the combined effect of the environmental and biological factors influenced the composition and distribution of the macroinvertebrate community in the hyporheic zone.