Abstract:With the development of medical disciplines and technological innovation, the knowledge related to microbiology is constantly developing and updating. We analyzed the problems emerged with the cutting-edge ideas and knowledge in the teaching of Medical Microbiology. These problems are caused by the new progress in research of microbiota and human health, evolution of microbial classification, updated understanding of microbial structure, contradiction between organ-system-based knowledge system and taxonomy-based knowledge system, etc. Furthermore, we discussed the possible solutions of reconstructing the teaching content, applying diversified teaching methods, and introducing the organ-system-based knowledge system. With the advancement of ‘New Medicine’ education in China, it is imperative to reform the teaching content of Medical Microbiology, so as to adapt to the development of medical disciplines and achieve the goal of talent cultivation.