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In the finite element analysis, large deformation caused by saturated sand liquefaction may lead to numerical problems owing to mesh distortion. Based on the soil–water two-phase mixing theory, the governing equations of the two-phase mixture are derived in the study. Using the operator splitting technique and the decoupled Arbitrary Lagrangian-Eulerian (ALE) frame, a decoupled ALE Finite Element Method is developed to solve the numerical problems caused by the possible mesh distortion in the liquefaction large deformation analysis. The method is applied to one-dimensional consolidation analysis and dynamic liquefaction large deformation analysis of an embankment. The results show that the method can keep the deformed mesh in a healthy state and ensure the accuracy of the numerical solutions in large deformation analysis.