This paper presents a fully coupled flow deformation model to characterize the nonlinear seismic site response of liquefiable marine sediments, considering the ocean wave environment. Emphasis is placed on extending a simplified soil hysteresis model for the effective stress analysis of nonlinear site seismic response. The proposed model addresses the limitations of existing one-dimensional (1D) hyperbolic soil models to simultaneously capture the 3D hysteretic stress–strain behavior and the accumulated volumetric deformation of soil skeleton. The volume strain formulation of soil skeleton is included in the Biot's volumetric compatibility equation as the source term for excess pore water pressure buildup. The proposed method is implemented into an explicit time matching finite difference analysis platform, and validated against the recordings of the KSRH10 site for North–South (NS) direction of KiK-net borehole arrays in Japan. Finally, the influences of ocean wave loading upon the seismic wave propagation behavior in liquefiable marine sediments are examined with reference to the Bohai Strait site condition, China. The obtained results indicate that the ocean wave environment has significant effect on the nonlinear seismic site response of liquefiable seabed at shallow depth.