Hongze Lake (HZL) is the largest impounded lake along the eastern route of China's South-to-North Water Diversion Project. However, there is surprisingly little ecological understanding on this important ecosystem, especially under the potential water diversion threats. Here, a mass-balance model was constructed to characterize trophic structure and ecosystem properties of HZL. The model outputs indicated that small sized fishes have dominated the food web, and fishery resources were suffered from high pressures of overfishing. Mandarin fish, Northern snakehead, Other piscivores and Large culters occupied the top trophic niche, while macrophytes, phytoplankton and detritus consisted of the main energy sources. HZL food web was fairly based on two main food chains: primary production (49.9%) and detritus pool (50.1%), but transfer efficiencies in both chains were relatively low as 6.37% and 6.49%, respectively. Predator-prey interactions, trophic cascading effects and competition of different components were also exhibited in the mixed trophic impacts map. Results from the network analysis suggested that the HZL ecosystem was a relatively mature ecosystem since the total primary production to respiration (TPP/TR) and to biomass (TPP/TB) were 1.138 and 6.922, and the Finn Cycling Index was 6.77%. Nevertheless, the relatively low values of Connectance Index (0.195) and System Omnivory Index (0.089), together with Finds Mean path Length (2.849) also indicated that the food web structure was vulnerable, characterized by linear, rather than web-like features. Our results suggested that the HZL ecosystem would be potentially affected by the future inter-basin water diversion, and thus ecosystem-based strategies were also presented accordingly.