The main purpose of this study is to newly develop a three-dimensional numerical model of multiphase flow “DOLPHIN-3D” using a CIP method and an extended SMAC method based on irregular mesh size grids, which introduces a DTM method of a highly accurate turbulence model based on the LES and the dynamic motion analysis of multiple rigid bodies. The validity of the model is verified by applying it to dynamic analysis of drifting bodies under wave actions and comparing with the laboratory experiments. The results reveal that the model is capable of simulating three-dimensional multiphase flows and time-changing wave pressures acting on drifting rigid bodies with high accuracy. The model would be, therefore, useful in discussing complex physical phenomena with solid-gas-liquid interaction.