In this paper, the pile-soil interaction of a low-rise pile cap foundation of an inclined straight alternating pile on two or three layers of a soil liquefaction site under seismic load is studied. By inputting the 0.5 g El Centro seismic wave in FLAC3D, the pile-soil interaction rule of the pile foundation of the inclined and straight pile groups of the low-pile cap under seismic action is simulated. By analyzing the soil acceleration, the pore pressure ratio, the horizontal displacement of the pile body, the vertical displacement, and the pile body bending moment, the law of pile-soil interaction between the pile and soil when the lower part of the pile is embedded in the clay layer is studied, and the low-rise pile cap inclined straight alternating group pile foundation on the two-layer soil and the three-layer soil free field is compared and analyzed. The results show that, under seismic load, the maximum acceleration of soil mass in the two-layer soil and three-layer soil model is discrete, and the pore pressure ratio of sand soil increases from bottom to top. By analyzing the displacement and bending moment of pile body, the bending moment at the joint between the pile cap and the top of pile body is the largest and the most vulnerable to damage. The maximum value of pile displacement and bending moment in the three-layer soil is less than the maximum value of the two-layer soil, indicating that the pile group foundation in the three-layer soil free site model is safer.