Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.