The earthquake-induced seabed instability is one of critical issues that need to be considered in the offshore structure design procedure. However, the investigations of the earthquake-induced seabed behaviour are limited. Most previous studies regard to the seabed response are adopting the traditional mesh-based method (such as finite element method). In this study, to overcome the drawbacks existing in mesh-based methods (for example, time-consuming and mathematical sophistication), a meshfree method is adopted to predict the soil response under the Japan 311 earthquake, based on the “u−p” approximation. The numerical results conclude that the earthquake-induced transient response, including the acceleration and the pore pressure were amplified from the top to the bottom of the seabed. The high values of the degree of saturation lead to a large magnitude of the pore pressures, while the amplification for the seismic wave become slightly extensive as the soil permeability increases.