Based on the survey data of fishery resources and ecological environment in the Jiaozhou Bay during 2015-2016, we developed a mass-balance model using Ecopath with Ecosim software for the Jiaozhou Bay. Using the Ecopath model, we evaluated the trophic structure,energy flow and ecosystem characters of the Jiaozhou Bay. The Jiaozhou Bay model consisted of 21 functional groups, and the fractional trophic levels ranged from 1 to 4.383. The mean trophic level of fishery catches in the Jiaozhou Bay ecosystem was 2.023, dominated by Manila Clam (Ruditapes philippinarum). The energy flow of the Jiaozhou Bay ecosystem was mainly dominated by grazing food chain, which accounted for 59% of the energy source. 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 16.35%, 16.22% from primary producer and 15.76% from detritus within the ecosystem. In addition, the ratio of total primary production/total respiration (TPP/TR) was 2.518, suggesting that the Jiaozhou Bay ecosystem was in an immature state.