The analysis and simulation of the interaction between groundwater and surface water is a considerably difficult problem in water resources planning and management.In this paper,a new approach for stream-aquifer system modeling is proposed.The interaction flow model based on stream leakage coefficient is coupled into the three dimensional numerical model.The variations of flow between stream and aquifers can be simulated and predicted under different stresses such as artificial groundwater recharge and withdrawal.The general formula for multi-layer aquifers system is also given in the paper.A case study illustrated that the coupled model is effective in groundwater numerical simulation and prediction.