The cumulative impacts of water conservancy projects in the Yangtze River basin, especially the Three Gorges Reservoir, have had a significant effect on the biological and ecological integrity of the Yangtze River estuarine ecosystem. This research establishes three ecopath models of the Yangtze River estuary and adjacent seas before (the autumn of 2000), during (the autumn of 2006), and after (the autumn of 2012) the impoundments of the Three Gorges Reservoir, using Ecopath and Ecosim software to characterize and compare the estuarine ecosystem's food web structure and energy flow. Sensitivity analyses were carried out to evaluate the uncertainty levels of the models. The three models consisted of 17 functional groups covering the main paths of the ecosystem food web, including piscivorous fishes, generalist predators, shrimp predators, zooplanktivores, crab predators, other pelagic fishes, other demersal fishes, other benthic fishes, shrimp, crabs, jellyfish, cephalopods, macrobenthos, meiobenthos, zooplankton, phytoplankton, and detritus. The simulated results showed that the values of trophic levels (TL) ranged from 1.000 to 3.802 in 2000 (before the impoundments), from 1.000 to 4.058 in 2006 (during the impoundments), and from 1.000 to 4.019 in 2012 (after the impoundments). This indicates that the TLs distributions of the functional groups were similar under all three conditions. However, the ecotrophic efficiencies of commercial species, such as Pseudosciaena polyactis, were elevated because of the increased fishing intensity in the Yangtze River estuary. The structure of catches did not change noticeably during this period, but the mean trophic level of the catch decreased from 3.406 to 3.369, as did the number of catches (from 1.026 t km^-2 a^-1 to 0.719 t km^-2 a^-1). Meanwhile, after the impoundments the role of the detritus food chain became less important to the energy transfer process than that of the grazing food chain, and over 90% of the energy flows were assembled in TL I and II, most of which flow into detritus and could be a source of internal pollution. The total transfer efficiency of the Yangtze River estuary ecosystem was 10.2% in 2000, 10.0% in 2006 and 9.4% in 2012. All of these negative effects are likely to be closely related to reductions in freshwater and sediment discharges, as well as the increase of land-based pollution in the Yangtze River Basin. Furthermore, the result also showed that the parameters of total biomass, total primary production, and the sum of all flows into detritus gradually decreased; however, the gross efficiency, Finn cycling index, Finn's mean path length, and system omnivory index increased. The ecosystems (before, during, and after impoundments) were found to remain in the immature stage.