Economic losses and property damage due to the failure of offshore structures are huge each year in the world, under the attack of endless conventional wave, occasional tropical storms or typhoons, and possible tsunami. Wave-induced dynamics of offshore structures and their seabed foundation attract a great deal of attention from researchers and ocean engineers. Previous literature investigated the wave–structures–seabed interaction generally adopting 2D models and decoupled way. In this study, taking a caisson breakwater as the typical offshore structure, the simple linear interaction between ocean wave, a caisson breakwater and its poro-elastic seabed foundation is investigated by utilizing a three-dimensional integrated numerical model FSSI-CAS 3D. The numerical results indicate that FSSI-CAS 3D can effectively and sufficiently capture a variation of phenomena of wave-induced dynamics of offshore structures, and momentary liquefaction in its dense poro-elastic seabed foundation. This study demonstrates great promise of using the developed integrated numerical model in offshore industry to predict the dynamic response and stability of offshore structures by ocean engineers in design stage.