Abstract: The Long-term wetting-drying cycles can weaken the engineering characteristics of subgrade fillers, resulting in engineering disasters. It is necessary to study the effects of the wetting-drying cycles on their microstructure and water-retention performance. A series of mercury intrusion tests, scanning electron microscopy tests, pressure plate tests and saturated salt solution vapor equilibrium tests considering the influences of the wetting-drying cycles are carried out on the subgrade filler of the existing ballasted track roads. The experimental results show that during repeated wetting-drying cycles, the soil structure is damaged, and the internal cementitious materials are continuously reduced. The number of micropores and small pores (< 5 μm) in the soil gradually increases, while the peak pore size in the range of mesopores and some large pores (5~30 μm) gradually decreases, and the distribution density gradually increases. After several wetting-drying cycles, the number of microcracks (> 100 μm) gradually increases, leading to cracking of the soil specimens. The wetting-drying cycles have effects on the water-retention characteristics of the soil. When the initial dry density is low, the air-entry value after experiencing one wetting-drying cycle is slightly higher than that without wetting-drying cycles, while the air-entry value of the specimen after three and five wetting-drying cycles continues to decrease.