Environmental Engineering Microbiology is one of the basic core courses of Environmental Engineering major in higher education in China, with the characteristics of short knowledge refresh period, numerous knowledge points and dispersive contents. In the process of teaching, how to strike a balance between traditional microbiology content and progress in modern microbiology research, choose the teaching content rationally, arrange the experiment project and experiment time reasonably, guide the students to grasp the basic concepts and knowledge points accurately, and train students’ hands-on ability, innovation consciousness and innovation ability are difficult problems for every teacher. Around the above-mentioned problems, our teaching team has taken some measures from the aspects of classroom and experiment teaching contents, teaching methods and extracurricular activities, and achieved better teaching results.