Industrialization has significantly polluted the Yangtze River Basin, posing phenolic compounds and heavy metals that threaten ecological and human health. This study comprehensively evaluated the impact of these pollutants on the Yangtze River's aquatic ecosystems across multiple trophic levels. Sampling from 84 sites during both dry and wet seasons, water chemistry and biological data were analyzed by advanced molecular and statistical techniques. All organisms are divided into three ecological functional groups with a multitrophic level structure based on their co-occurrence. Our results demonstrate pronounced spatial and seasonal variations in pollutant concentrations, with notable sensitivity in ecological structures to phenolic compounds and heavy metals. The ecological impacts of pollutants are more readily observable (up to 43.1 % maximum) when assessing ecological communities based on functional groups with multi-trophic biological community as opposed to traditional taxonomic classifications. All the data used to develop a predictive model for ecological functional groups, achieving an accuracy rate of 86.1 %. This research provides critical insights into the multi-trophic effects of composite pollution, advocates for the adoption of comprehensive multi-trophic evaluation methods in large-scale ecological monitoring and sustainable watershed management globally.