The phenomenon of liquefaction is one of the most important subjects in Earthquake Engineering and Coastal Engineering. In the present study, the governing equations of such coupling problems as soil skeleton and pore water are obtained through application of the two-phase mixture theory. Using a up (displacement of the solid phase-pore water pressure) formulation, a simple and practical numerical method for the liquefaction analysis is formulated. The finite difference method (FDM) is used for the spatial discretization of the continuity equation to define the pore water pressure at the center of the element, while the finite element method (FEM) is used for the spatial discretization of the equilibrium equation. FEM-FDM coupled analysis succeeds in reducing the degrees of freedom in the descretized equations. The accuracy of the proposed numerical method is addressed through a comparison of the numerical results and the analytical solutions for the transient response of saturated porous solids. An elasto-plastic constitutive model based on the non-linear kinematic hardening rule is formulated to describe the stress-strain behavior of granular materials under cyclic loading. Finally, the applicability of the proposed numerical method is examined. The following two numerical examples are analyzed in this study: (1) the behavior of seabed deposits under wave action, and (2) a numerical simulation of shaking table test of coal fly ash deposit.