Abstract: Oral Microbiology is a vital component of the basic science of stomatology and an important compulsory course for undergraduate students of stomatology, focusing on the oral microbiology and microecology, the pathogenesis of oral infectious diseases, and the relationship between oral microbes and human health. Our faculty team have made reforms of the theory and laboratory teaching of the course Oral Microbiology. We have introduced in the classroom the concept of Three Comprehensive Approaches to Education—the full involvement of everyone, the through-course approach and all-round education—and offered inquiry-based instruction through a combination of extracting the core information from every chapter, using the core information as the foundation, integrating the core information with clinical problems, and using experiment operation to foster in the students an attitude of solving clinical problems through research. These teaching innovations improved the undergraduate students’ motivation to learn. We evaluated the teaching effect with questionnaire surveys. The results suggested that the students showed high interest in learning and were satisfied with our teaching innovations. In addition, student performance evaluation for the course showed significant improvement, indicating that the instructional reform program of Oral Microbiology was conducive to students’ understanding and mastery of the course content, improved student motivation to learn and their grades, and received positive reviews from the students. We report herein, from three aspects, the course innovations and the experiences gained. We discussed the significance of integrating ideological and political theories teaching in all courses and using innovative teaching materials and teaching models and, highlighted their importance in the education of stomatology students, and proposed suggestions to further improve the course design of Oral Microbiology.