Soil erosion is one of the most serious problems that threaten the safety of embankments and earth-rock dams. When water flows through the base soil, fine particles subjected to hydrodynamic action will be washed away, which will lead to internal erosion of the embankment project. The inverted filter structure is one of the effective methods to eliminate or reduce the risk of infiltration and erosion, with a history of nearly a century of engineering practice. This article is based on the three-dimensional LBM-DEM fluid solid coupling simulation method. By setting different particle size ratios and hydraulic gradients in the filter medium, the particle contact erosion and subsequent migration and transportation of fine particles in the filter layer structure were comprehensively reproduced, verifying the effectiveness of traditional empirical formulas. This study demonstrates the effectiveness and feasibility of the three-dimensional LBM-DEM coupling method in practical engineering applications from a microscopic view, laying the foundation for the next large-scale simulation of embankment filter layers and the revelation of microscopic mechanisms.