Mining areas characterized by high underground water levels are one of the most important types of coal mining areas in China. In regions with high groundwater levels, the soil ecological environment is destroyed due to surface subsidence induced by coal mining and soil disturbances. There are a variety of soil factors each with different degrees of spatial variation, and the impact on soil microbial communities is particularly severe. In order to explore the change and driving mechanism of soil microbial community structure in coal mining subsidence areas with high underground water levels, we sought to elucidate these mechanisms by studying soil samples collected at different depths (SL: 0-20 cm, ML: 20-40 cm, DL: 40-60 cm) of a deep coal seam subsidence area (T1) and shallow coal seam subsidence area (T2) and their control non-subsidence areas (W1 and W2) within a typical coal mine area with high underground water levels in southwest Shandong Province. These soil samples were used for determination and analysis of their physicochemical properties and microbial diversity. The results show that coal mining subsidence has significant effects on the soil physicochemical properties and soil microbial community. With the increase in sampling depth, the soil water content (SWC), bulk density (BD), and soil pH increased, whereas the contents of soil alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), available potassium (AK), and soil organic matter (SOM) decreased. Compared with the non-subsidence area, the soil alkalinity in the subsidence area was lower and the soil moisture content, affected by the underground water level, was higher; the richness and diversity of the microbial community was lower in the subsidence area despite its higher relative abundance of Actinobacteria, Chloroflexi, and Myxomycota species. In addition, species of Thelebolales and Pleosporales were dominant in T1 and T2, respectively. Soil pH was observed to be the most important physicochemical factor affecting microbial communities, followed by AN and AP. The results of our study provide a theoretical basis for soil ecological restoration and land reclamation in mining areas with high underground water levels.