This paper probes into the reform of the course of Microbiology under the background of applied universities, so as to highlight the characteristics of applied universities and to train higher applied talents. Taking the undergraduate students majoring in biological engineering in Jing Chu University of Technology as the research objects, the teaching mode of Microbiology has been innovated and reformed through the comprehensive application of teaching methods, such as rearrangement of teaching contents, micro-lesson production, case teaching and flipping classroom. The results of teaching and questionnaire survey in the experimental group and the control group show that, compared to the traditional one, the new teaching model is more conducive to the students' mastery and application of knowledge.