In the reform of medical microbiology education on medical students of 8-year-education program, we compared the traditional teaching methods with Problem Based Learning (PBL) method. Through our practice, we have found that the combination of traditional lecture-based learning and PBL seems to better match the students’ way of learning. The lack of basic knowledge of the students hindered their learning effect during the bilateral discussion in the PBL education. We also found that the application of PBL in medical microbiology education is an iterative process and should be promoted step by step. The theoretical level and the innovative ideas of the teachers play a crucial role in the dynamic process of education reform.