In this study, a semi-coupled 3-D numerical model for fluid-structures-seabed-interaction is developed. The dynamic Biot's equation known as "u-p" approximation, and modified Navier-Stokes equation in which the linear drag force between the flowing pore water and the solid matrix of porous medium is included, is respectively adopted as the governing equation in the soil sub-model and the wave sub-model. A coupling algorithm is developed to integrate the two sub-models together, in which non-match mesh and non-match time scheme are used based on the shepherd interpolation method. The data exchange is implemented at the interface between fluid domain and seabed/marine structures domain adopting the coupling algorithm. Finally, the developed 3-D numerical model is validated by an analytical solution and a laboratory wave flume test.