Environmental Engineering Microbiology is one of the core subjects in the environmental engineering major. It is also one of the pre-subjects for its professional subjects. In order to improve the teaching effect, the comprehensive experiments, the productive practice experiments, and the research experiments were added based on the verification experiments. Combined with the course practice and graduation project, the practice teaching system had been gradually reformed and improved. As a result of this, a teaching mode of “Integrated Practical Teaching System (IPTS)” was constructed. It had been proved that this model could stimulate students’ interest in learning, practical ability, innovation consciousness, and ability to analyze and solve problems.