This work developed a numerical model to investigate the interaction of water waves and offshore structures. The model solves three-dimensional (3-D) spatially averaged Navier-Stokes equations. The Large-Eddy Simulation (LES) technique was applied to reveal the behavior of the associated turbulent flows. The governing equations were solved based on a multi-block Cartesian grid system (Chimera grid system) (English et al., 2013). In order to reduce the computational time, the proposed 3-D numerical model was established in a GPU-based parallel computing environment. The proposed numerical model was applied to simulate the 3-D lid-driven cavity flow and the wave fields induced by a solitary wave past a vertical circular cylinder. The good agreement of our numerical results with available numerical results and experimental data verifies the accuracy of the proposed 3-D numerical model.