Abstract: In order to provide basic information for protecting and rational utilizing resources of the Yangtze Estuary, feeding types, trophic level, energy flow, and food web, 43 aquatic animals were studied by using stomach content analysis. The species were classified into four groups according to their feeding habit: plankton feeding, benthic feeding, nekton feeding, and mixed feeding (benthic and nekton feeding). Among the samples collected in this study, the plankton predators were dominant accountings for 39.53%, and the nekton predators had the minimum dominancy, accounting for 11.63%. The results of trophic level showed that according to the dietary habits, these aquatic animals can be also divided into 3 different groups, which herbivorous consumers were dominant, and accounted for 76.75%, while intermediate carnivorous fish had the minimum dominancy, accounting for 4.65%. Through the overfishing and environmental degradation, the trophic levels of the 12 common fish in the Yangtze Estuar were generally lower than those of the 1990s, the average trophic level dropped from 3.80 to 2.87. According to each consumer’s stomach content, this study determined the benthic algae and phytoplankton, and organic detritus, including particulate organic matter (POM), as the main producers of the Yangtze Estuary aquatic food web, and drew their own energy flow. Eventually, based on the nutritional relationship among different aquatic animals, this study proposed a simplified model for the Yangtze Estuary aquatic animals’ food web.