Abstract: Ecopath with Ecosim (EwE) is designed for straightforward construction, parameterization and analysis of mass-balance trophic models of aquatic ecosystems. Base on the data from environments, resources and ecology survey in Daya Bay during 1984~1986 and 1986~1987, the energy flow model of ecosystem in Daya Bay is constructed using the EwE package. According to the characteristic of the food composition of swimming animal in Daya Bay, the ecosystem comprised 15 function groups, which are marine mammals, carnivorous fish, benthic-feeding fish, zooplanktivorous, herbivorous fish, crabs, shrimps, cephalopods, zoobenthos, jellyfish, zooplankton, corals, submerged plant, phytoplankton and detritus, respectively. And the function groups can cover the main trophic flow of the ecosystem in Daya Bay. The result shows that the trophic level of the function groups varied from 1.0 to 3.88. The transfer efficiencies for each trophic level are 7.2%, 11.2%, 8.7%, 2.9%, respectively. The transfer efficiencies can be used for constructing a figure presenting the trophic flows in form of a pyramid. The total transfer efficiency of Daya Bay's ecosystem is 8.9%, less than that of Lindeman (about 10%), perhaps a lot of submerged plant (Sargassum) in Daya Bay can not be utilized fully, and decayed and broke down. In course of the energy flow, the proportion of total flow originating from detritus is 48%, and from primary producer is 52%.