Quality-oriented education of new era college students needs not only have enough theory knowledge, but also has cultivates on scientific thinking and training on application skills. For the purpose to enhance the quality-oriented education, a teaching mode system was developed based on innovation practice on the microbiology course. Among this, an innovation mode with synchronous training, that is, theoretical instruction, skills training, and subject practice was the key step of the system. During the implementation of the program, the results of the innovation practice were included in final grades to force the undergraduates to take part in. A three-way interaction training, that is, teachers, graduate students, and undergraduates, was developed. The target and the technical route of the practice were made by our teacher. The topic selection, conceptual design, and the research process of the subject were directed by graduates. And the experiment program, results analysis were finished by undergraduates. The results indicated that this is helpful for thinking-way formation, skills improvement, and the innovatory consciousness development of the undergraduates. And this is a useful way for quality education for our university students.