Abstract: As a commonly used port structure, caisson wharves may undergo translation, settlement, tilting and other disasters due to sand liquefaction under seismic loads. The conventional finite element method may not correctly reflect the seismic response of caisson wharves due to the distortion of the grid caused by the liquefaction deformation under strong earthquakes. Based on the operator splitting technique, this paper develops an ALE finite element method for the dynamic liquefaction analysis of caisson wharves with two types of foundations under three types of seismic loads. The results show that the ALE method provides accurate and reliable seismic response of the caisson wharves under strong earthquakes and ensures the overall grid quality. The residual displacement of caisson is linearly related to the peak seismic load and more sensitive to low-frequency seismic loads. The high pore pressure connecting regions between the replaced region and backfill region may increase the residual displacement of the caisson wharves. Measures should be considered to block the pore pressure transfer channel.