Rapid urbanization in the Xiamen Bay area has greatly changed ecosystem productivity and other eco-service function of wetland ecosystems. A simulation model was developed based on system dynamics and analytical causal-loop feedbacks to quantify the cumulative ecological effects of the change for the Xiamen Bay City, including its hydrological dynamics, water quality, ecological characteristics, geomorphic features, and landscape structure. The cumulative ecological effects of alternative policies were simulated by adjusting the decision-making variables and their combinations, and quantitatively assessed by using the grey model (GM), followed by model verification and sensitivity analysis. The consequences of three scenarios for future management were simulated and compared, including baseline scenario (BS), the eleventh Five-Year Plan scenario (S1), and the eco-city scenario(S2). The cumulative ecological effects indices were 0.61, 0.37, and 0.30, respectively, for the BS, S1, and S2 scenario. The cumulative ecological effects under S2 scenario was 50% of the BS scenario. Consequently, we recommend Xiamen adopt the eco-city (S2) model for its future development.