With the unstructured grid, the Finite Volume Coastal Ocean Model (FVCOM) is converted from its original FORTRAN code to a Compute Unified Device Architecture (CUDA) C code, and optimized on the Graphic Processor Unit (GPU). The proposed GPU-FVCOM is tested against analytical solutions for two standard cases in a rectangular basin, a tide induced flow and a wind induced circulation. It is then applied to the Ningbo’s coastal water area to simulate the tidal motion and analyze the flow field and the vertical tide velocity structure. The simulation results agree with the measured data quite well. The accelerated performance of the proposed 3-D model reaches 30 times of that of a single thread program, and the GPU-FVCOM implemented on a Tesla k20 device is faster than on a workstation with 20 CPU cores, which shows that the GPU-FVCOM is efficient for solving large scale sea area and high resolution engineering problems.