Considering graduate students under diverse knowledge background in the first level discipline-Environmental Science and Engineering, this study aims at constructing a comprehensive graduate course system of Microbial Physiology in the interdisciplinary context. The feedbacks regarding the course were collected through questionnaire. Based on questionnaire, the teaching content, methods and assessing mode of Microbial Physiology were reformed. An appropriate course system of Microbial Physiology was constructed, and the issues such as separation of basic knowledge of microbial physiology from practical application were solved and it could improve the efficiency of teaching. The enthusiasm and initiative of students were inspired, which helped students have a better command of knowledge. Above all, the cultivation quality of graduated students was considerably enhanced as expected.