The physical and chemical processes of polycyclic aromatic hydrocarbons (PAHs) are coupled with their ecological dynamic processes by using Delft3D model in the Hulushan Bay, Dalian. Based on in-situ monitoring data and previous references, the characteristic parameters for the ecological dynamics processes of PAHs are set and the corresponding simulated work is carried out. Here, the growth rate of phytoplankton is selected as an indicator of ecosystem health in coastal waters, and the numerical simulation results of PAHs concentrations are fitted with the dynamics response equation of the growth rate of phytoplankton to quantitatively evaluate the effect of PAHs on marine ecosystems. The result shows that when the sewage outfall is located at such a place with deep water, fast flow rate and strong hydrodynamic condition, it will benefit the diffusion of PAHs, and thus improve the water quality. On the contrary, it will result in the serious enrichment of PAHs in the Hulushan bay. In addition, the enrichment of PAHs has a significant influence on the ecological environment in the Hulushan Bay. The poor hydrodynamic conditions lead to that the reduction of 18% in the growth rate of phytoplankton. Finally, spatial GIS analysis demonstrates that the reduction in the growth rate of phytoplankton does not agree with the spatial distribution of PAHs concentrations well, reflecting the dynamic complexity and ecological stability of the ecosystem in the Hulushan bay.