The human-oriented education is the central idea of scientific development view. According to the characteristics of the bioengineering students, this paper presented the reform and practice on the teaching method of Microbiology, including guiding ideology, teaching content and teaching method. The teaching practice proved that the new pattern of Microbiology education not only stimulated students’ interest in studying the course, but also developed their creative capability and the comprehensive quality. So it meets the demand of social development during the new period.