An integrated Finite Element Method (FEM) model is proposed to investigate the dynamic seabed response for several specific pipeline layouts and to simulate the pipeline stability under waves loading. In the present model, the Reynolds-Averaged Navier–Stokes (RANS) equations are used to describe the wave motion in a fluid domain, while the seabed domain is described using Biot's poro-elastic theory. The interface between water and air is tracked by conservative Level Set Method (LSM). The FEM and backward differentiation formula (BDF) are applied for spatial and temporal discretization respectively in the present model. One-way coupling is used to integrate flow and seabed models. The present model is firstly validated using several available laboratory experiments. It is then further extended to practical engineering applications, including the dynamic seabed response for the pipeline mounted on a flat seabed or inside a trench. The results show that the pipeline buried to a certain depth is better protected than that under partially buried in terms of transient liquefaction.