Abstract: Daya Bay, located in the eastern Guangdong Province, is an important economic region. Human activities such as fishing and waterway transportation have changed its ecological structure and function. Thus, assessment and sustainable utilization of fishery resources require study on the interaction among functional groups in the ecosystem. In the present study, Ecopath with Ecosim (EwE 6.4) software was applied to study the energy flow, general characteristics and food web structure in the whole ecosystem. Daya Bay has two main channels of food chain (grazing food chain and detritus food chain). The conversion efficiency among trophic levels in Daya Bay ecosystem was relatively low, the total energy transfer efficiency being just 8%. The total system throughput of the ecosystem was 6 249.573 t·(km²·year)^-1. The total production was 2 827.584 t·(km²·year)^-1. The total net primary production was 2 468.36 t·(km²·year)^-1. The ratio of total primary productivity to total respiration (TPP/TR) was 2.185. Finn′s cycling index and the mean path length of the energy flow were 4.8% and 3.53, respectively. Connectance index and system omnivory index were 0.324 and 0.174, respectively. To sum up, the Daya Bay ecosystem is at an immature stage which has a simple food web, low maturity and poor stability. It is needed to enhance fishing restriction and improve environmental protection.