A box model based on nitrogen balance for fish-shellfish-macrophytes polyculture in coastal embayment was developed, and applied for Xiangshan Harbor, China. Simulated phytoplankton, zooplankton and nitrogen concentration were consistent with the measured data of Xiangshan Harbor. The results showed that the seasonal variation of biological production rate led to the mutual transformation of nutrients (such as nitrogen) between dissolved inorganic form and detritus form, and the transformation showed an obvious annual oscillation. The phytoplankton reached the peak amount in summer and showed the lowest amount in winter, while the DIN exhibited an opposite variation pattern. Total nitrogen input into Xiangshan Harbor was about 2 182 tonN/a, coming equally from aquaculture and sewage. The nitrogen output from the bay was,by decreasing order,water exchange with ambient water, aquaculture harvest and fishing. At present, the nitrogen input is larger than the output (about 11%), causing the DIN concentration increase of about 42μgN/L per year in the bay. The model was used to analyze long-term (20 years) influence of different polyculture modes on the DIN concentration in the bay. It shows that DIN concentration in Xiangshan Harbor will slowly increase and the input of nitrogen tends to be balanced with output for the coming several years under current aquaculture mode. If the fish culture is reduced to 40% of the current scale or the macrophytes culture is increased about 20 times of the current scale, the DIN concentration in the bay would gradually decrease and fit the national Grade Ⅲ water quality standard in about 14 years.