Soil health is the central theme of sustainable agricultural development. Soil microorganisms cooperatively drive the soil life system by regulating soil ecological functions, environmental functions and immunologic functions, which are the keys to maintaining soil health. Understanding the mechanisms of soil microorganisms mediated soil health is essential to effectively utilize these core microorganisms to maintain and improve soil health. Thus, soil functions, such as soil carbon cycling, nutrient cycling, soil structure regulation, plant disease and insect inhibition and contamination control mediated by soil microorganisms are reviewed to summarize their roles in maintaining or enhancing soil health. Furthermore, as a sensitive indicator of soil health, the roles of soil microorganisms in soil health indication and warning were also studied. Research about mining, construction and application of the core microbiome information database that drives the specific function of soil health and multiple biological processes should be strengthened in the future. This will help to provide a scientific basis for improving the function of agricultural soil ecosystems using soil microorganisms, maintaining soil health and soil sustainable development.