The structure of a caisson breakwater has been necessary to have registance against Tsunami. For the verification of the designing of caisson, SPH-DEM simulation is hoped to play a critical role as a numerical method used instead of hydraulic experiment. As a numerical method, we develop two models for interaction between SPH and DEM. One is non-permeable model that is for impermeable structures to water such as caisson. The other one is permeable model that is for permeable structures to water such as riprap mound. To apply this numerical method to large-scale 3D model, the high performance computing is necessary for SPH-DEM simulation. In this research, the computational speed is improved by parallelizing the simulation code using GPU. This simulation is applied to Tsunami overflow analysis, and the applicability of the simulation method is validated by comparing to the experimental result.