Objective To explore the effect of a case-based learning method in the teaching of medical microbiology. Methods One hundred and sixty undergraduates from 8-year program of clinical medicine enrolled in 2016 and 2017 in Peking Union Medical College (PUMC) joined this research. Controlled trial method was applied in the study; 86 students from grade 2017 were assigned to the experimental group and 74 from grade 2016 to the control group. The experimental group was intervened with case-based learning, while traditional teaching was applied in the control group. Final exam analysis of both groups and anonymous questionnaires from the experimental group were used to evaluate the teaching effects. Results The scores of final exam of the experimental group and control group were (61.4±3.8) and (59.7±4.4) respectively(P＜0.05).The new teaching method was thought to be effective facilitation of basic knowledge into clinical use by 90.7%(78/86) students as well as stimulation of students' learning interests by 84.9%(73/86) students. Conclusions Case-based learning can support students' learning, promote the understanding of occupational application of knowledge in future and thus stimulating students' learning interests.