The critical thinking is an ability to value the theory and the objective existence according to the full reason and objective facts. The critical thinking training for the students not only can help them to improve the ability to adapt to the information society, but also can cultivate their creative spirit and ability. In Microbiology teaching, the ways to train the students’ critical thinking are as follows: Studying the contents of teaching, cultivating the critical spirit. Designing the open exercises, encouraging the creative thinking. Setting the debating activities, training the critical skills. Offering the evaluating opportunities, improving the evaluating abilities.