In response to the significant ecological damage caused by unsustainable mining practices in the Qilian Mountains, ecological restoration projects have been undertaken in recent years. Analyzing the changes in soil microbial communities during the restoration process of mine meadows helps to reveal the mechanism of the restoration process in alpine mining areas. To explore the characteristics of soil microbial community distribution and their relationships with soil environmental factors during the restoration of alpine grasslands in the Qilian Mountains, we conducted surveys and analyses in two restoration levels low restoration (LR) and high restoration (HR) in the eastern Qilian Mountains, along with an undisturbed natural grassland control (NG). We found that as the degree of high-altitude mining area recovery increases, there were significant increases in vegetation cover, vegetation height, above-ground biomass, vegetation Shannon–Wiener index, soil organic carbon (SOC), soil water content (SWC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available phosphorus (AP), and available nitrogen (AN). Conversely, soil pH and electrical conductivity (EC) significantly decreased, with soil pH decreasing from 6.93 to 4.13. Restoration of high-altitude mining area grasslands significantly alters the distribution and composition of soil bacteria and fungi, while the impact on soil microbial community changes was not significant. Notably, with increasing recovery level, the dominant bacterial phyla are Acidobacteria and Proteobacteria, while the dominant fungal phyla are Ascomycota and Basidiomycota. These results indicate that changes in vegetation and soil properties both affect the composition of soil microbial communities, with soil properties having a greater influence. Soil fertility and nutrient levels emerge as the primary drivers influencing soil microbial composition communities and the degree of high-altitude mining area grassland recovery.