Temporary freshwater rock pools, as special, small-sized and isolated habitats, provide ideal systems for studying island biogeography and ecological theories and processes. In this study, a total of 70 potholes of mountain rivers were sampled during the four seasons from November 2013 to October 2014 to assess the structure of the benthic invertebrate community and to identify the relationships between habitat characteristics and the community composition. Pothole area ranged from approximately 0.01 to 0.39 m², and pothole depth ranged from 0.03 to 0.74 m. Forty-three taxa belonging to 37 families and 16 orders were collected from the potholes. The highest numbers of benthic invertebrate taxa were observed in summer and the highest average number of taxa per pothole (8.5) was observed in autumn. The diversity was the highest in spring, and the average densities of benthic invertebrates were highest in autumn. Large potholes supported more taxa than small ones and significant relationships between richness and pothole area, richness and water volume were observed. The results of Redundancy Analysis show that the community composition of benthic invertebrates in the potholes was closely correlated with water temperature, pothole area and water depth. Our results indicate that benthic invertebrate communities in river potholes are mainly structured by water depth, pothole area and water volume. The seasonal changes are also an important factor determining the presence/absence of certain taxa.