In order to improve the teaching effect of Food Microbiology and promote students to develop scientific epistemology and methodology, the materialist dialectic views, such as diversity and unity, commonality and individuality, absoluteness and relativity, external and internal factors, were applied throughout teaching practice. In addition, more scientific teaching content and process can be designed according to the perspective of dialectics. The application of materialist dialectics not only changed the students’ way of thinking, but also enhanced the intrinsic and logical link of course contents, and hence it obviously improved the teaching effectiveness.