Abstract: Based on the generalized vertical coordinate,an unstructured grid numerical method is developed to simulate three-dimensional shallow water flow. The semi-implicated finite difference and finite volume discretization are applied to the momentum equations and conservation equation,such that the model is robust,stable and mass conservation is satisfied both locally and globally. Since unstructured mesh and generalized vertical grid,the proposed numerical model is well suited to fit complicated estuaries and coastal boundaries and yet is sufficiently flexible to set the vertical layers. The test cases of wind-driven currents and lock exchange flow are used to demonstrate the model's capabilities. Comparisons between numerical results and analytical data are presented. The Pearl River Estuaries is modeled and is verified and calibrated with field measurement data. The computed results mimic the field data well.