In this paper, based on the centrifuge test of liquefied soil-pile foundation system, a numerical model of liquefied soil-pile foundation-structure system is modelled by using OpenSees platform. In the simulation model, the friction effect between liquefied ground and low pile cap is considered, and the method of establishing virtual nodes is used to deal with the non-linear contact between liquefiable soil and low pile cap. The rationality and effectiveness of the numerical simulation method adopted in this paper has been verified and evaluated by comparing with the results of centrifuge experiments. A typical liquefaction soil-pile integrated finite element model is modelled using validated numerical simulation methods. The law of seismic response of the pile foundation system with different embedding depths of pile cap, different contact modes between the pile cap and saturated sand, and the thickness of the overlying saturated loose sand layer are discussed. The results show that the pile cap and pile foundation in the high pile cap system show higher seismic response characteristics than the other three low pile cap system conditions; Under the condition of different contact modes between the pile cap and the surrounding saturated sand, the peak bending moment and residual displacement of the pile foundation calculated by the bond contact are larger than calculated by the friction contact, and the deformation of pile is more significant. By comparing the working conditions of different thicknesses of overlying saturated loose sand layer, it is found that the degree of liquefaction in shallow soils is less affected by thickness of the saturated loose sand. As the thickness of saturated loose sand layer increases, the peak bending moment and residual displacement at the top of the pile also gradually increase. The change of peak bending moment at the soil interface is more obvious.