Abstract: Stock enhancement is important for conservation of exploitable resources. Assessment of ecological capacity of the discharged sea area before discharge and planned implementation of proliferation and discharge activities can avoid damage to the original ecosystem. Based on the survey data of the fishery resources of Pearl River estuary in 2016, an Ecopath mass-balance model of the Pearl River estuary ecosystem consisting of 29 functional groups was constructed. Thus, the overall characteristics of the ecosystem, the food-web structure and the mixed trophic impact were analyzed. The ecological carrying capacities of six species of stock enhancement which were suitable for this area were estimated. The results show that the fractional trophic levels ranged from 1 to 4.2, and those of the six species ranged from 2.2 to 3.7, with marine mammals occupying the highest trophic level. The total system throughput of the ecosystem was 9 092.447 t·(km²·a)^–1, and the total energy transfer efficiency was 12.23%. The connectance index and system omnivory index were 0.370 and 0.287, respectively. There were two main channels of food chain in the ecsystem, and the energy flow was dominated by grazing food chain. The ecological carrying capacities of biomass for Lateolabrax japonicus, Acanthopagrus schlegelii, A. latus, Penaeus penicillatus, P. monodon and Paphia undulata were 0.094 t·km^–2, 0.500 t·km^–2, 0.650 t·km^–2, 1.580 t·km^–2, 1.610 t·km^–2 and 75.870 t·km^–2, respectively.