The microbial manufacturing industry is developing rapidly in China owing to the policy of “green production, energy saving, and emission reduction”. This industry involves agriculture, food, energy, chemical, and other fields and generates great economic benefits and social values. In this article, we describe the development trend of the global microbial manufacturing industry, summarize the development status of China’s microbial manufacturing industry in the fields of fermented food, biological fertilizer, enzyme preparation, bio-based material, and biomass energy, and analyze the opportunities and challenges of the industry in China. The research technology of China’s microbial manufacturing industry is constantly reforming and innovating, the production level of some major fermentation industries ranks among the top in the world, new strains and products continue to increase, and the scale of industrial production is gradually expanding. However, China’s microbial manufacturing industry still lacks independence regarding core strains, cutting-edge scientific research technologies, and key production equipment. Moreover, we suggest that China’s microbial manufacturing industry should improve its independent research and development capabilities, strengthen cross-industry innovation, develop intelligent equipment for industrial production, and accelerate the transformation of scientific research results.