The ecological problems caused by coal mining in Yellow River Basin are becoming more serious. In order to explore the influence characteristics of coal mining disturbance on soil factors and microbial community in Yellow River Basin, and to clarify the differences in soil microbial communities between the marginal coal mining subsidence area and the unmined area, equidistant sampling was performed from the marginal subsidence area, the start point (HD), to the unmined area in the study area of Shangwan Mine in Inner Mongolia. Specifically, sampling points at 150 (D1), 300 (D2), 450 (D3), 600 (D4) and 750 m (D5) from the marginal subsidence area were selected to measure the three soil factors (nutrient indicators, soil enzymes and soil C∶N∶P stoichiometric characteristics) and the microbial communities. The results show that the difference of soil factors and microbial diversity between the marginal subsidence area and the unmined area is mainly concentrated in the unmined area closer to the marginal subsidence area (less than 300 m). The total nitrogen, organic matter, and bacterial abundance of soil decrease in varying extent in the region near the marginal subsidence area, while the available potassium, carbon to nitrogen ratio (C/N), and the activity of sucrase and phosphatase increase in varying extent. Regarding the composition of microbial community, the relative abundance of Acidobacteria in the unmined area increases at first and then decreases with the increasing of distance. The relative abundance of Chloroflexi in the marginal subsidence area is higher than that in the unmined area. Further, the relative abundances of Phaeosphaeriaceae and Chaetomiaceae in the marginal subsidence area are significantly higher than that in the unmined area. It is found through the study that the influence of the marginal subsidence area on the unmined area is mainly concentrated within the area close to the marginal subsidence area (within 300 m). The diversities of bacteria and fungi are more sensitive to soil factors. Besides, the key taxa are correlated with the soil factors in varying degrees. In the future, more attention should be paid in the artificial restoration to the marginal subsidence areas and its influence on unmined areas, and the artificial means should be applied to the key affected areas, so as to achieve a better restoration effect.