A 3D two-phase flow model is developed to deal with the free surface problems by the surface capturing method. The numerical approach to solve the governing equations is based on the finite volume method for space discretization. To take into account the discontinuity properties of fluid density near the free surface, the TVD-MUSCL scheme is employed to overcome unphysically numerical oscillations. On the other hand, the explicit 4-stage Runge-Kutta scheme is employed in the model for discretization in time. In order to enhance the computational efficiency of the model for simulations of 3D large-scale and complicated geometry problems, the domain decomposition method based on multi-block grid system is adopted and incorporated with message passing interface (MPI) library for parallel computation in this study. The experimental data of the dam-break problem are used to validate the proposed model with parallel computation for unsteady flow problem. The comparison of the efficiency of parallel computation under different grid numbers is presented and discussed. In addition, the model is applied to simulate the oblique hydraulic jump in the contracted entrance of the Yuan-Shan-Tzu flood diversion channel for steady flow problem. The influence of different zonal strategies on the computational time is also investigated.