The microbial industry is a strategic emerging industry and it is an important field for developing new growth drivers and for creating new global competitive advantages. In the face of the great opportunity to promote the construction of Healthy China, the development of the microbial industry is significant for regional scientific and technological innovation, high-quality industrial development, and improvement of people’s welfare in China. The study expounded the macro-demand for the development of microbial industry and analyzed the development status of the global microbial industry in terms of industrial layout and technological progress. The study further outlined the development trend of the microbial industry in China from the aspects of industrial policy environment and industrial scale, investigated the development status of industrial segmentation directions including microbial safety, microbial health, microbial manufacturing, and microbial medicine, and dissected the challenges in the development of the industry. Our findings indicated that structuring systematic big science facilities, developing a series of industrialized technologies, and promoting the industrial application of microbial resources are key initiatives to accelerate the development of the microbial industry in China. We proposed to strengthen the research and development of key core technologies of the microbial high-tech industry, promote the establishment of an industrial policy system for collaborative innovation and development, and build industrial clusters centering around microbial innovation platforms, all of which will greatly improve the development level of microbial industry in China.