Abstract: Using a WRF atmospheric model and a 3-D ocean numerical model FVCOM based on finite volume method， a three-dimensional numerical model of storm surge within Lianyungang shallow waters is developed. The 3-D storm surge during typhoon WIPHA is simulated by use of different turbulence models such as k-ε and MY-2.5. The simulation results of the 3-D storm surge flow and vertical turbulence viscosity coefficient are analyzed in the study. The analysis results show that， compared with the poor results from MY-2.5 model， the vertical velocity and direction distribution of the storm surge calculated by k-ε model has a good agreement with the measured data， and the values of the vertical turbulence viscosity coefficient are crucial for the vertical structure of the storm surge， therefore a right turbulence model is preferred. The k-ε turbulence model is suggested for simulation of the 3-D storm surge in the future.