Food web structure dynamics and ecosystem functioning are strongly linked, and both are indispensable in evaluating ecosystem development in lakes under multiple anthropogenic stressors. However, model-based approaches concerning the changes in food web structure and ecosystem functioning in a certain lake during distinct periods are scarce. In this study, we focus on Lake Chaohu, the fifth-largest lake in China, which has undergone drastic changes over the last several decades. Data from the 1950s, 1980s and 2000s were used to create three Ecopath mass-balance models. These Ecopath models were validated by the stable isotope-determined trophic level (TL) for each functional group, which indicated an acceptable model performance. Over time, we observed a collapse of the food web toward a simplified structure and decreasing biodiversity and trophic interactions. The lake ecosystem was approaching an immature but stable status from the 1950s to the 2000s, as indicated by the multiple related indicators and the distribution of energy flows in slow detrital-based and fast primary producer-based channels. We further discuss the potential driving factors and underlying mechanisms, hypothesizing that hydrological regulation may play a significant role in driving all of these changes in Lake Chaohu in addition to eutrophication and intensive fishery. Overall, we strongly advocate the identification of a threshold in abundance of zooplanktivorous fish, an integrated strategy for future ecological restoration in Lake Chaohu, and the consideration of using Ecopath as a new management tool for other lakes, thereby bridging the strategies from both environmental and ecological perspectives.