As an indispensable part of the lifeline for the offshore gas and oil industry, submarine pipelines under long-term marine environmental loadings have historically been susceptible to earthquakes. This study investigates the impact of trench backfilling on the residual liquefaction around a pipeline and the induced uplift of a pipeline under the combined action of an earthquake, ocean wave and current loading. A fully coupled nonlinear effective stress analysis method, which can consider the nonlinear hysteresis and the large deformation after liquefaction of the seabed soil, is adopted to describe the interaction between the seabed soil and the submarine pipeline. Taking a typical borehole in the Bohai strait as the site condition, the nonlinear seismic response analysis of the submarine pipeline under the combined action of seismic loading and ocean wave and current is carried out. The numerical results show that trench backfilling has a significant impact on the seismic response of the pipeline. The existence of trench backfilling reduces the accumulation of the residual excess pore water pressure, so that the seabed liquefaction around the pipeline is mitigated and the uplift of the pipeline is also decreased.