Veterinary Microbiology is one of the most important basic courses in veterinary medicine related majors. In order to cultivate the innovative high-quality talents, we have carried out the teaching reform of Veterinary Microbiology. The reform was started with the teaching idea, teaching mode, and the examination system. The teaching-centered lectures have been turned to guiding student to the autonomous learning. Furthermore, various teaching methods were integrated flexibly into each knowledge point, and the whole process comprehensive examination system was implemented to test both knowledge and ability. By putting these into practice, students’ initiative learning enthusiasm and learning interests were aroused, and students’ independent learning ability, creative thinking ability, as well as practical ability were cultivated. The reform has changed students’ attitude toward learning that focusing on results rather than process. The practice has showed positive outcome on teaching efficiency, suggesting the transform is worth popularizing.