Different layers of soil often have distinct particle sizes. When exposed to the natural environment, soil is easily affected by natural rainfall, rising groundwater levels, and human activities, leading to particle contact erosion, which reduces the safety and service performance of the soil structure. In this paper, a coupled computational fluid dynamics–discrete element method (CFD–DEM) model was employed to investigate the particle migration phenomena, mechanical response of contact interfaces, variations in flow fields, and macroscopic deformation during the contact erosion process under cyclic loads at different frequencies and amplitudes. The conclusions are presented as follows: (1) Within one cycle of cyclic loading, both compression during loading and stress relaxation during unloading are the main factors triggering the migration of fine particles. (2) The migration and loss of fine particles mainly occur in the early stages of cyclic loading, where strong contact force chains are formed within the fine particle layer, leading to significant plastic deformation of the soil at the macroscopic level. (3) Under cyclic loading, changes in the soil pore structure cause an upwards hydraulic gradient in the initial quiescent water flow field. This hydraulic gradient can rupture weak contact force chains and cause particle pumping. (4) Increasing the frequency and amplitude of cyclic loading intensifies the erosion of fine particles, causing greater axial deformation of the soil. Compared to cyclic loading frequency, the amplitude of cyclic loading has a greater impact on contact erosion.