Industrial biotechnology aims at transforming discoveries of life science into products, processes, systems, and services, which creates new opportunities for economic developments and is regarded as an important research field worldwide. Fermentation engineering is a key field of industrial biotechnology, which is rebuilding fermentation and light industry. In this paper, we systematically summarized four innovation tasks of fermentation engineering, including transformation and upgrading of bulk fermented products, energy conservation and emission reduction of traditional industries, solving safety issues of food processing, and biomanufacturing of functional nutraceuticals. Finally, development trends in fermentation engineering were discussed. The future development of fermentation engineering will be facilitated by technology and equipment systems for fermentation intelligentization and new industrial mode based on fermentation intelligentization.