In this paper, based on centrifuge shaking table model tests of liquefied site-pile foundation system, a numerical model of the liquefied site-low pile cap-pile group system is established by using OpenSees. The nonlinear contact problem between pile cap and soil is realized by establishing virtual nodes in the numerical model. The effectiveness of the numerical simulation method used in this paper is verified by the monitoring results of centrifuge test. Based on the verified numerical modeling method, a two-dimensional integrated numerical model of liquefied soil-pile structure system is established with the actual liquefied site engineering as the background. The influence of the embedding depth of pile cap, the contact of liquefaction soil-low pile cap and the thickness of overlying saturated loose sand on the liquefied soil-pile foundation system are also discussed. The results show that the peak bending moment and residual displacement of pile in the high pile cap-pile system is larger than that in the low pile cap-pile system. The results of the residual displacement and peak bending moment at pile head calculated by the bond contact method are higher than the calculated by the friction contact. Under different overlying saturated loose sand thickness, the peak bending moment between pile head and the soil interface increases with the increase of the soil thickness. Particularly, the mutation of peak bending moment at the soil interface is gradually obvious with the increase of the soil thickness.