The sea water intrusion has water-rock interactionprocess and spatial variability of geological parameters, which makes it difficult to calculate the intrusion process. The paper proposed a method combining GIS and 3D finite element method to simulate and analyze the sea water invasion process. The GIS is developed using database and component techniques, improving the data organization efficency. 3D finite element model adopts proper parameters from multi layers of GIS, decrease the error of the parameters selection. The dynamic seepage-diffusion coupling mechanism is also considered in the study. The seawater intrusion in NanGuanling region of Dalian City has been studied by the method. The calculation results of both flow and chlorine ion distribution field are all coincidence with actual observation well information. That stated the simulation method is feasible. The numerical simulation of next three years is also carried out and it showed that the seawater encroachment area will decrease. That means the amount of exploited groundwater in the past years is reasonable. The conclusion has active supervise meaning to prevention and cure of seawater encroachment in the area.