To improve students' initiative in learning through integration of basic and clinical medicine has become an important goal and direction of medical education reform. Since 2018, Tianjin Medical University has implemented the teaching reform of medical microbiology in five-year program of clinical medicine including the organization of teaching team, implementation of multiple teaching methods, construction of online course platforms, optimization of experimental training content and of evaluation system. The courses are systematically taught for key teaching content. The flipped classroom teaching is adopted for some courses and comprehensive designed experiments as well as virtual simulation experiment platforms are introduced to experimental training. The teaching effect was evaluated by final examination and questionnaire survey. The results showed that the passing rates of students from grade 2016 to 2018 are 55.6% (99/ 178), 61.4% (102/166) and 88.4% (153/173), respectively. Majority of students[86.2%(112/130)]believed that multiple teaching methods were very suitable and 99.2% (129/130) of the students acknowledged that their self-learning ability has been improved or significantly improved. The teaching reform scheme of medical microbiology was conducive to students' understanding and mastery of basic knowledge and to the improvement of students' autonomous learning capacity.