In the process of using transportation infrastructure, contact erosion between different particle sizes soil layers can easily occur under complex hydro-mechanical coupling, leading to deformation and damage of structures. To investigate indirect erosion between soil layers under cyclical load effects from a microscopic perspective, a volume of fluid-discrete element method (VOF-DEM) coupled method was adopted in this study. The influence of different water table levels and particle size ratios (PSR) was considered. The study found that: (1) The compressive effect of coarse particles during loading and the stress relaxation effect during unloading can both cause migration of fine particles within one loading-unloading cycle; (2) Immersion of the contact surface between coarse and fine particles is a key factor in inducing particle migration, with the interaction between particles being the most intense at the contact surface; (3) Fully saturated soil experiences the most severe particle erosion and macroscopic deformation; (4) Reducing PSR can effectively improve the integrity of soil structure and suppress erosion of fine particles; (5) Particle migration inevitably leads to axial deformation of the soil, resulting in reduced stiffness and increased energy dissipation during loading-unloading cycles. This study provides new insights into contact erosion under complex hydraulic coupling from a microscopic perspective.