To improve the quality of environmental microbiology course, flipped classroom was carried out in Nanjing University. The teaching content lay more stress on basic microbiology to provide necessary prerequisite to the scientific consideration of Environment Microbiology, whilst the arrangement of knowledge point underline the combination of microbiology with enviromental problems. The reform in course content could help to the differentiated instruction on applied technology and research talent. In the reform of teaching model, heuristic, interactive and investigated teaching methods were adopted in class. The flipped classroom was applied to increase the student’s participation in autonomous learning through interaction with students. The flipped classroom reform of Environment Microbiology lay emphasis on “learning” through feedback teaching to improving the comprehensive appreciation and application of Environment Microbiology.