High-intensity coal mining has induced a series of ecological and environmental problems issues, including surface subsidence, the development of ground cracks, and the deterioration of vegetation. The disruption of water circulation systems induced by mining, such as perched groundwater, groundwater of aeration zone, and phreatic water, is the root cause of vegetation withering. The aeration zone serves as a crucial nexus in the process of water cycling and exerts a significant influence on soil fertility. To explore the characteristics of soil moisture transport in subsidence areas under the mining disturbance, on-site monitoring of the size and morphology characteristics of subsidence areas and ground cracks was conducted in typical mining areas in Inner Mongolia, China. Subsequently, a typical soil moisture transport model was constructed in subsidence areas, the soil moisture transport patterns under the influence of different types of subsidence and cracks were analyzed, and the influence law of soil damage on soil moisture transport in the aerated zone was clarified. The results indicate that (1) Based on the occurrence and distribution characteristics of subsidence cracks, the subsidence area can be divided into tension zone, compression zone, and neutral zone; the ground cracks are divided into permanent tension cracks and dynamic cracks. (2) The drought stress effect of soil in the subsidence area is significant. Under the influence of soil structure variation, the water-holding capacity of the soil in the subsidence area decreases, and the soil moisture dissipation is strong. The soil moisture transport rate in the aeration zone of the subsidence area is ranked as follows: tension zone > neutral zone > compression zone. (3) Ground cracks can exacerbate the soil moisture transport rate in the aeration zone. After 15 d of crack appearance, the soil moisture transport reaches a relatively stable state, and the soil moisture transport rate in the surface layer of the crack is the fastest, and the loss of soil moisture is the most significant. The crack effect is not significant beyond 100 cm from the crack. This study provides a theoretical and data support for soil and vegetation remediation in mining subsidence areas.