Zooplankton is generally affected by both top-down and bottom-up regulations in aquatic ecosystems. However, the relative strength of top-down and bottom-up controls on zooplankton assemblages is not well understood. Here, we analyzed this question in five lakes of the Yangtze River basin, an area with high population density and thousands of lakes, many of them suffering multiple environmental pressures. We sampled the whole communities of five lakes in the middle reaches of Yangtze River basin from 2006 to 2011 and used structural equation modeling to evaluate the relative importance of joint top-down and bottom-up effects. With increasing total phosphorous (TP), a major shift occurred in trophic structure. Biomass of phytoplankton, rotifers, cyclopoids, and planktivorous fish significantly increased, while cladocerans and calanoids were negatively correlated with increasing TP. The bottom-up effects were strongest at the bottom of the food web (e.g., effects of TP on phytoplankton). Direct bottom-up effects of phytoplankton and other food resources (latent variable) on rotifers and cyclopoids were greater than top-down controls from planktivores. The predation pressure on crustacean zooplankton by planktivores was higher than that on rotifers. In planktivore-dominated systems, piscivores only played a marginal role, whereas they seem affected by water quality. These results suggest not only in the food web processes the important role of nutrient pollution in affecting the top of the food web in these lakes, but also that the impacts and relative strength of bottom-up and top-down controls may vary with zooplankton assemblages, indicating the complexity of food webs in degraded lakes in China ; We thank Sabine Giessler, the editor, and two anonymous reviewers for helpful comments and suggestions on the manuscript. This work was supported by a Special Fund for Agro-scientific Research in the Public Interest (Grant No. 20130356); the R and D Project of the Ministry of Science and Technology of China (Grant No. 2012BAD25B08); and Projects of the National Natural Science Foundation of China (Grant Nos. 30830025 and 31201994). Financial support to EGB was provided by the Spanish Ministry of Economy and Competitiveness (Project CGL2013-43822-R), the Government of Catalonia (Ref. 2014 SGR 484), and the European Commission (Erasmus Mundus Partnerships "TECHNO'' and "TECHNO II'')