Body size is sensitive to environmental changes and recognized as one of the fundamental traits linking ecological functions. Recently, size structure has been suggested as a useful indicator for environmental monitoring and assessment in aquatic ecosystems. However, the organisms’ size structure and the relationship with environmental factors remain seldom addressed in reservoir ecosystems. In this study, firstly, we investigated the zooplankton community composition and size structure, including the slope of the normalized biomass size spectrum (NBSS) and size diversity in the Xiangxi Bay of Three Gorges Reservoir, China. Then we analyzed how the environmental factors affect the zooplankton abundance and size structure (NBSS slope and size diversity) by using the structural equation model (SEM). In terms of the community composition, rotifers were the predominant zooplankton group in the Xiangxi bay during the whole research period, which abundance is significantly higher than protozoan, cladoceran, and copepod (Mann-Whitney U tests, P < 0.001). For the size structure, both the slope of NBSS and size diversity showed high spatiotemporal dynamics. The slope of NBSS ranged from − 2.201 to -0.097, and the size diversity ranged from 0.631 to 3.291. And lowest values of NBSS slope and size diversity were observed in the upstream areas of Xiangxi Bay. Further analyses based on SEMs found a clear pathway revealing how nutrient variables affect the zooplankton abundance and size structure. That is, dissolved inorganic nitrogen had an indirect effect on the zooplankton abundance, NBSS slope, and size diversity by affecting the phytoplankton biomass. In addition, SEM found that water temperature had a significant negative effect on the size diversity but had nonsignificant effects on zooplankton abundance and NBSS slope. This finding suggests that size diversity is a useful index in measuring the zooplankton size structure. Our study highlights that size diversity is a robust indicator for environmental monitoring and assessment, especially in complex and dynamic reservoir ecosystems.