The migration of fine particles to coarse particle assemblies and the resulting clogging have a significant impact on ground and foundation performance such as stone columns and granular filters during earthquakes. In particular, complex effects besides seepage will occur and exacerbate particle clogging under earthquake loadings. In this study, a coupled numerical simulation method including Finite Difference Method (FDM), Discrete Element Method (DEM) and Computational Fluid Dynamics (CFD) is proposed to simulate the response of granular material, to explore the fine particles migration and clogging, and the driving of hydraulic gradients respectively under cyclic loadings. The calculation example shows that a previous shaking event could reduce the drainage capacity of coarse particle assemblies and increase the risk of soil liquefaction during the subsequent shaking event.