Metabolic Engineering is a core course for undergraduate and graduate students major in Bioengineering. Whether it is “intelligent manufacturing” for emerging industries or the upgrade of traditional fermentation industry, this course can reflect the characteristics of the Emerging Engineering. Metabolic Engineering is more focused on cultivating students’ ability to comprehensively use professional knowledges to solve practical problems, that is, to rationally design metabolic pathways and regulatory networks to achieve the “bio-intelligent manufacturing” of the target products. Based on the comprehensive, time-effective, and applied characteristics of Metabolic Engineering, we have clearly defined the course goals, focused on classic content, followed the discipline development, highlighted practical application, and emphasized teacher-student interaction to continuously optimize the teaching system and teaching content. In this course, we also put forward a variety of teaching ideas such as “laying stress on the succession of teaching contents”, “inspiring students’ thinking through typical cases”, “displaying cutting-edge developments of the discipline”, and “summarizing the important teaching contents”. In the teaching process, this course has effectively stimulated students’ interests in learning, enhanced their learning effects, and layed a solid foundation for the cultivation of high-level Emerging Engineering innovative talents.