Microbiology is an important part of life sciences. With the rapid development of science and technology, the teaching content and teaching methods of microbiology need to be constantly updated to meet the requirement of high-quality personnel training. In the teaching of microbiology, Huazhong Agricultural University has been actively carrying out the teaching reform practice based on the cultivation of innovative ability. We have tried to promote students’ scientific spirit in the classroom through the respect of academic celebrities, through paying more attention to the social focus to stimulate learning interest, through introducing cutting-edge disciplines, training and innovation awareness to actively guide students to learn the relevant knowledge of microbiology. By flipping the classroom and divided class, with the help of “micro-teaching aids” WeChat public platform, we have challenged the traditional teaching model to enhance the interaction between teachers and students and to break the limitations of time and space of student learning to strengthen exchanges between teachers and students. Depending on the State Key Laboratory of Agricultural Microbiology and other high-level research platform, we have further encouraged students to enter the laboratory with microbiological knowledge to carry out scientific research practice, guide students to participate in various competitions, in order to transform the theoretical knowledge into practical innovation ability. In short, students can not only firmly grasp the knowledge of microbiology in the classroom, but also get trained in their innovative thinking to significantly enhance their creativity.