In order to systematically study the meso-mechanism of piping failure of embankment foundation caused by overlying coarse-grained soil layers, the PFC3D and angle of repose calibration method were used to calibrate the model. The relationship between macro-parameters of materials and meso-parameters of particles was established quickly and accurately. The development process of seepage deformation of coarse-grained soil was simulated effectively, and the meso-parameters and migration rules of seepage deformation were obtained. We found that when the fine material content in the overlying coarse-grained soil layer was 10% and 20%, the fine particles moved among the framework particles and lost under the action of water pressure, which was manifested as piping failure. The less the fine material content in the overlying coarse-grained soil layer, the more easily the fine sand layer is destroyed. When the fine material content was 30%, the flow-soil failure occured near the piping mouth, and then the large particles of coarse-grained soil in the upper part and the fine particles of the fine sand layer lost synchronously and gradually developed upstream, resulting in piping failure, and the whole particle loss process presented transitional seepage failure. When the overlying coarse-grained soil layer was piping soil, the large particles of the upper coarse-grained soil had a rapid settlement under the action of head pressure. When the overlying coarse-grained soil layers were transitional soils, the initial subsidence of the overlying coarse-grained soil layers did not occur, and the subsidence of the overlying coarse-grained soil layers began gradually after the flow-soil failure occurred, and the subsidence of the overlying coarse-grained soil increased with the decrease of the fine material content in the framework particles of the overlying coarse-grained soil. This study provides a reference for the calibration of meso-parameters in the numerical simulation of three-dimensional particle flow, and reveals the influence of the fine particle content in the overlying soil layer on seepage deformation and the migration law of particles.