In this study, a new medical microbiology experiment teaching system, which was based on outcome-based education combined with inquiry-based teaching model, was developed and evaluated. According to the professional requirements of doctors, the objectives of emotion and comprehensive experimental ability were added, and the requirement for experimental operation skills was raised. In accordance with the concept of inquiry-based teaching, experimental contents were reorganized, and practical operation contents and comprehensive analytical experiments were increased to facilitate students' abilities of independent thinking and innovation. In addition, the proportion of microbiology laboratory examination was increased, experimental skill examination was focused, the assessment method was reformed, and extracurricular interest groups were established to deepen the learning. The teaching effect was evaluated by questionnaire, performance and follow-up survey. The result showed that the new model increased the students' course scores, improved their capability in innovation, academic writing and clinical working, and strengthened the weakness of traditional teaching in application and exploration, providing a new idea for the reform in medical microbiology experiment teaching.