Abstract: Based on the survey data of the Yangtze Estuary fishery resources and ecological environment survey in spring (May) and autumn (November) in 2020, the Ecopath model of the Yangtze Estuary ecosystem was established to analyze the ecosystem structure and energy flow characteristics of the Yangtze Estuary before the total fishing ban of the Yangtze River. The model consisted of 17 functional groups, including Harpadon nehereus, Coilia mystus, Coilia nasus, tongue sole, zooplankton feeding fish, benthic feeding fish, swimming feeding fish and omnivorous fish, which basically covered the energy flow process of the Yangtze Estuary ecosystem. The results showed that the trophic level of the Yangtze Estuary ecosystem ranged from 1.000 to 4.438, with the highest trophic level of Harpadon nehereus and the trophic level of other fish ranging from 2.907 to 3.768, which was widely distributed. The trophic levels of benthos, molluscs, shrimp and crabs were concentrated from 2.365 to 2.826. The energy flow distribution of each trophic level in the Yangtze Estuary ecosystem mainly concentrated in trophic level Ⅰ to Ⅱ, and the energy flow from trophic level I accounted for the highest proportion of the total energy flow in the system. The energy flow of the Yangtze Estuary ecosystem was mainly transferred by the grazing food chain. Compared with the past, TPP/TR value of the Yangtze Estuary ecosystem in 2020 was higher, while CI value and SOI value increased, but were still less than 1, indicating that the Yangtze Estuary ecosystem was still immature and in the development stage.