A decoupled ALE method is developed based on operator splitting technique and soil water two-phase mixture theory and applied to the seismic response analysis of subway station in saturated sand in this research. It is found that the Rayleigh damping coefficients have a remarkable influence on the deformation shape, the final floating, and the acceleration response of the underground structure, which needed to fully consider the influence factors to avoid over-damping or under-damping of the system. The comparison of the seismic response of the subway station from the UL method and the proposed ALE method verifies the applicability of the method for such problems. Additionally, the ALE method is utilized to the seismic response of the subway station in deep loosed sand in the case of mesh distortion in the UL method. The results show that the ALE method ensures the mesh quality and the solution accuracy of the model. Owing to the subway station uplift, the ground near the subway station uplifts, while settles far away from the station, and the higher the earthquake intensity, the wider the range of the ground affected to uplift. The development of excess pore pressure ratio in the soil is synchronous with the corresponding Arias intensity. The uplift of the subway station could be divided into initial floating stage and fast floating stage, and the excess pore pressure ratio triggering the structure into initial floating stage and fast floating stage falls in a range rather than a threshold, except for the complete liquefaction site. The liquefied sand flows to the beneath of the subway station is the primary factor causing the structure to uplift. Moreover, the Ratcheting mechanism, Pore pressure migration mechanism, and the Viscous flow mechanism all contribute to the subway station floating. It is found that the increase of the buried depth will approximately linearly decrease the floating of the subway station, the vertical excitation has little effect on the floating of underground structure, while the densification of soil on both sides and beneath the subway station can significantly decrease the floating rate and floating of the subway station.