In this paper we developed a mass-balance model (Ecopath) using Ecopath with Ecosim software for the northern South China Sea (NSCS, 107°00′-120°00′ E、17°00′-23°30′N). Input data were mainly from the information collected in marine ecology surveys during 2007-2008. Using the Ecopath model, we evaluated the trophic structure, energy flow and system attribute，and briefly summarizes the characteristic of the over-fishing ecosystem also. The balanced model suggests that the system was dominated by the grazing food chain; with primary producers serving as a principal source of energy in the system. Fractional trophic levels ranged from 1.0 to 3.99, with marine mammals occupying the highest trophic level. The mean trophic level of fishery catch in the NSCS ecosystem for the 2007-2008 was 2.93. Using network analysis, the system network was mapped into a linear food chain and six discrete trophic levels were found with a mean transfer efficiency of 11.5%, 10.4% from detritus and 12.6% from primary producer within the ecosystem. In this study the Connectance index (CI) and system omnivory index (SOI) were 0.290 and 0.239, respectively. A Finn cycling index (FCI) of 4.380 and mean path length (MPL) of 2.476 were obtained also. Furthermore, the ratio of total primary production/total respiration (TPP/TR) was 2.596 in the system. We can conclude that, therefore, the system is still immature and instable through analysis and discussion. This paper also briefly summarizes the characteristic of the over-fishing ecosystem.