Micro-organisms play important roles in promoting soil ecosystem restoration, but much of the current research has been limited to changes in microbial community structure in general, and little is known regarding the more sensitive and indicative microbial structures or the responses of microbial diversity to environmental change. In this study, based on high-throughput sequencing and molecular ecological network analyses, the structural characteristics of bacterial communities were investigated in response to four different ecological restoration modes in a coal mining subsidence area located in northwest China. The results showed that among soil nutrients, nitrate-nitrogen and fast-acting potassium were the most strongly associated with microbial community structure under different ecological restoration types. Proteobacteria, Actinobacteria, and Acidobacteria were identified as important phyla regarding network connectivity and structural composition. The central natural recovery zone was found to have the smallest network size and low complexity, but high modularity and good microbial community stability. Contrastingly, a highly complex molecular ecological network of soils in the photovoltaic economic zone existed beneath the photovoltaic modules, although no key species, strong bacterial competition, poor resistance to disturbance, and a significant increase in the relative abundance of Gemmatimonadetes were found. Furthermore, the reclamation zone had the highest soil nutrient content, the most complex network structure, and the most key and indicator species; however, the ecological network was less stable and readily disturbed.