The excess pore water pressure (EPWP) generated under the combined vertical and horizontal earthquake excitations is generally greater than that under the unidirectional excitation, which may further affect the dynamic response of soil-pile-superstructure-quay wall (SPSQ) system. This study conducted a coupled effective-stress analysis for the response of SPSQ system to liquefaction-induced lateral displacement under horizontal and vertical earthquake excitations. To accurately describe the lateral displacement behind the quay wall, the liquefaction behavior of soils was described by a modified generalized plasticity model with parameters properly determined from laboratory tests. The numerical model of the SPSQ system was validated against the previously reported centrifuge model tests. The results show that the earthquake excitation with abundant low-frequency component causes greater residual lateral displacements of footing (ux,RF) and quay wall (ux,RQ ) than that with abundant high-frequency component. The ux,RF and ux,RQ tend to increase as the peak vertical acceleration increases for both vertical and inclined piles. Increasing the fixity of the quay wall significantly reduces the influence of vertical ground motion on the ux,RF and ux,RQ. The polarity reversal of the vertical ground motion also has a significant effect on the ux,RF and ux,RQ and should be considered in the analyses. In addition, the lateral displacement of liquefied ground causes an amount of rotation of the cap of the inclined pile, probably leading to the potential shear failure at the head of piles.