Understanding the effects of global warming on trait variation and trophic structure is a crucial challenge in the 21st century. However, there is a lack of general patterns that can be used to predict trait variation and community trophic structure under the ongoing environmental change. We investigated the responses of body size and community trophic structure of zooplankton to climate related factors (e.g., temperature). Isotopic niche breadth was applied to investigate the community trophic structure across a 1‐year study from a subtropical reservoir (Tingxi Reservoir) in southeastern China. Body size and community isotopic niche breadth of zooplankton were larger during water mixing than stratification periods and correlated significantly with water temperature change along the time series. The contributions of intra‐ and intertaxonomic components to body size and community trophic structure variation showed significant relationships with the temperature change going from the mixing to stratification periods. Water temperature imposed direct effect on body size, while direct and indirect effect on the community trophic structure of zooplankton occurred through trophic redundancy along time series. Water temperature and community properties (e.g., body size, trophic redundancy, or trophic interaction) showed complex interactions and integrated to influence community trophic structure of zooplankton. Our results can expand the knowledge of how elevated temperature will alter individual trait and community trophic structure under future climate change.