Agricultural microbial industry is a kind of biotechnology industry and high value-added agriculture formed by using agricultural microbial resources and biotechnology, involving in many fields such as planting, breeding and agricultural environment. Agricultural microbial industry is now becoming an important growth point of national strategic emerging industries, which plays vital roles in ensuring national food security, improving the quality of cultivated land and increasing agricultural emission reduction. The purpose of this paper is to study the development strategy of agricultural microbial industry, to elaborate the characteristics, pain points and opportunities of industrial development, and to put forward suggestions and countermeasures. The results show that microorganisms and their related technologies have become the key way to solve the sustainable development of agriculture in China: the breakthrough of basic research and key technologies has promoted the agricultural microorganisms into a new round of technological revolution; the exploration and utilization of microbial resources has reached a new stage; the subdivision industries have ushered in a period of rapid development opportunity. At the same time, China's agricultural microbial industry is also faced with problems such as low rate of core strain autonomy and sharing, relatively weak basic research, and lagging product development. It is suggested that China's agricultural microbial industry should strengthen source innovation, break through cutting-edge key technologies, accelerate the construction of national microbial germplasm resources scientific equipment, and build a new platform for scientific and technological innovation and industrial development.