To study the influence of the drying–wetting cycles on the subgrade filler structure and dynamic characteristics of existing ballasted track subgrade, a series of mercury intrusion tests, scanning electron microscopy tests, and dynamic triaxial tests were carried out considering the drying–wetting cycles. The results indicate that drying–wetting cycles can gradually increase the number of micropores, small pores, mesopores and microcracks in the soil, leading to volume shrinkage and cracking. Under cyclic loading, the accumulated axial strain increases exponentially with the number of drying–wetting cycles. The critical cyclic stress decreases exponentially with the increase of drying–wetting cycles. With the increase of the number of drying–wetting cycles, the resilient of the specimens under cyclic loading continues to weaken. When the number of drying–wetting cycles is greater than 5, the phenomenon of “false increase” of resilient modulus will occur due to the large accumulated axial strain. The drying–wetting cycles has a significant effect on the structure and dynamic characteristics of clay subgrade filler. It is necessary to take a series of measures to ensure the safe and stable operation of existing ballasted tracks in response to the effect of drying–wetting cycles.