In order to enhance the ability of emergency response to storm surge disaster and ensure moistureproof safety, the 3D unsteady k-ε model coupled with the volume of fluid (VOF) method of water-air two-phase flow is established. The model adopts the method of equivalent roughness to deal with urban intensive building groups, in which the effect of water resistance and water storage are both taken into consideration. One hundred years frequency storm surge is analyzed based on the numerical simulation and analysis of floodwater evolution with storm tide between the Haihe River and the Yongdingxinhe River of the new coastal region of Tianjin. The severity of different frequencies of the storm surge are compared and analyzed. The results show that the flooded area and the water depth decrease with the increasing of storm surge frequency. The researches provide theoretical foundation and technical support for the safety management of the sea wall and scientific assessment of storm surge disaster.