Using a 1982 model of the Bohai Sea as the starting state, an Ecosim model was constructed for the Bohai Sea, including the 17 functional groups. Using time series of catch per unit effort (CPUE) and relative fishing effort as the driving factors, this model simulated the dynamic changes in different developmental stages of the Bohai Sea ecosystem and the impact of fishing on this ecosystem. The effects of climate change on the fishery resources of the Bohai Sea ecosystem were analyzed based on the environmental time series data. From 1982 to 2008, the biomass of Oratosquilla oratoria showed an increasing trend, and the biomasses of some species of high economic value showed decreasing trends, including Pseudosciaena polyactis, Scomberomorus niphonius, Engraulis japonicus, Lateolabrax japonicus, and Setipinna taty, and the biomasses of shrimp, crabs, and cephalopods were relatively stable. The mean trophic level of the catch clearly decreased from 1982 to 2008, and correlated significantly negatively with the total catch. The fishing-in-balance (FIB) index followed the same trends as the total catch, increasing after 1984. The Q-90 diversity index fluctuated slightly from 1982 to 1987, maintaining a growth trend in 1988-1994, followed by a rapid decline after 1994, from 2.5 to around 0.5, and the fishing biodiversity decreased. The surface salinity, surface temperature, and Yellow River runoff significantly affected the fishing yield in the Bohai Sea. A comparison of the initial (1982) and end states (2008) of the model showed that the maturity of the ecosystem decreased. Overfishing resulted in the degeneration of the ecosystem and a decline in the total biomass. Thus, fishing and environmental changes were the main factors affecting the changes in the fishery resources in the Bohai Sea ecosystem.