Considering the impact of the subgrade water level and freeze-thaw cycles, experiments were conducted on ballast track subgrade mud pumping. The study analyzed the migration of water and fine particles, as well as the characteristics of mud formation during the mud pumping process of the ballast track subgrade under cyclic loading. The research findings indicate that, during the initial loading stage at ambient temperature, moisture migrates upwards from the bottom. As dynamic loading is continuously applied, the internal pore water pressure in the subgrade soil gradually dissipates, resulting in a decrease in the pore water pressure gradient and a stabilization of the moisture content in each soil layer. When the water level is positioned in the middle of the subgrade, the upper soil is in an unsaturated state with a relatively low volumetric water content of approximately 26%. Fine particle migration does not occur, and the effective stress at the subgrade surface is much greater than zero, thus preventing mud pumping. When the water level is at the top of the subgrade, particle migration is more pronounced. The effective stress at the subgrade surface rapidly decreases to below 0 under the action of the load, resulting in mud pumping phenomena. Compared to unidirectional freezing, freeze-thaw loading results in a slower descent rate of the freezing front and a greater amount of moisture migration. Under thawing conditions, the upper soil layer of the subgrade thaws before the lower soil layer, forming a frozen soil interlayer. Due to the isolation effect of the frozen soil interlayer, the upper soil layer retains a higher moisture content. Under the action of the load, the effective stress at the subgrade surface rapidly develops into negative values, making it more susceptible to mud pumping.