The wave-seabed-pipeline interaction problem is particularly important for coastal geotechnical engineers involved in the design of submarine pipelines. Most previous investigations have only concerned with the soil response due to linear progressive ocean waves, even though strong evidence of wave non-linearity has been reported in the literature. In this study, the finite element model (GFEM-WSSI) proposed by the first author is adopted to investigate the interaction between nonlinear ocean waves, a buried pipelines and a porous seabed. Unlike previous models, the deformation of pipeline and non-homogeneous soil behavior are also considered in the new model. Numerical results demonstrate that the influence of non-linear wave components can not always be ignored without committing substantial error, especially for the case of large waves in shallow water. Also, revealed is that nonlinear wave-induced seabed response is affected significantly by variable permeability and shear modulus. Moreover, the internal stresses of buried pipeline increase significantly with a decrease of pipeline thickness.