The experiment of Medical Microbiology is an important bridge for the theoretical knowledge of Microbiology and clinical practice, and occupies an important position in the teaching of Medical Microbiology. However, in the traditional experimental courses confirmatory experiments are mostly presented, and neither the learning effect nor teaching effect is satisfactory. In this paper, the interdisciplinary comprehensive experimental teaching model is discussed, which is based on the relevant knowledge in related disciplines. Related theoretical knowledge is integrated efficiently in this new teaching model, and could also be closely linked to clinical practice in future. This new teaching model could overcome the disadvantages in traditional teaching, greatly inspire the enthusiasm and initiative of students, and effectively improve the ability of independent thinking and comprehensive analysis abilities of students.