This paper deals with a computational method with multiphase-modeling to predict the 3D free- surface flows through porous media consisting of multiple solid particles like the ground water flows in coarse gravel. In contrast to most of the previous methods, in the present method, the fluid-cells, which are sufficiently finer than the solid particles, are set up in the computational domain and the fluid-solid interactions are accurately calculated by a multiphase-modeling method that needs no empirical parameters such as the drag coefficient Cd. In addition, a parallel computational method is implemented on the basis of the 3D domain decomposition method using MPI. The predicted results are compared with experimental values and further applicability of our method is examined through the numerical experiments for the porous media consisting of randomly-arranged spheroids.