In this study, based on the dynamic Biot's theory "u-p" approximation, a 3D finite element method (FEM) numerical soil model is developed, in which the Generalized Newmark-method is adopted to determine the time integration. The developed 3D FEM soil model is a part of the coupled model PORO-WSSI 3D for 3D wave-seabed-marine structures interaction problem, and is validated by the analytical solution proposed by Wang (2000) for a laterally infinite seabed loaded by a uniform force. By adopting the developed 3D soil model, the consolidation of seabed under a caisson breakwater and hydrostatic pressure is investigated. The numerical results show that the caisson breakwater built on seabed has very significant effect on the stresses/displacements fields in the seabed foundation after the transient deformation and primary consolidation are completed. The parametric study indicates that the Young's modulus E of seabed is the most important parameter to affect the settlement of breakwater, and the displacement fields in seabed foundation. Taking the consolidation status as the initial condition, the interaction between ocean wave, caisson breakwater and seabed foundation is briefly investigated. The 3D ocean wave is determined by solving the Navier-Stokes equations with finite volume method (FVM). The numerical results indicate that there is intensive interaction between ocean wave, caisson breakwater and seabed foundation; and the breakwater indeed can effectively block the wave energy propagating to the coastline.