Microbiology is an important basic subject. Reform of classroom teaching model of microbiology plays an important role in the cultivation of innovative talents in life sciences. Case teaching is an effective method for stimulating students’ interest and improving students’ initiative in learning. In the case teaching in microbiology, the sources of cases can be varied. Cases with local characteristics and around students are more effective for stimulating students’ interest in learning. Based on case type and teaching aim, case-based teaching in microbiology can be divided into three types. Case teaching can not only promote the opening and interaction of teaching, but also plays an important role in the value guidance of the students.