Objective To examine the effects of a new pedagogy of application of minimally invasive surgery (MIS) to clinical medical students in topographical anatomy.Methods Clinical medical students were randomly divided into two groups, traditional group taught by traditional topographical anatomy pedagogy and minimally invasive surgery group taught by the new pedagogy of clinical minimally invasive topographical anatomy. Results Compared to students in traditional group, students in minimally invasive topographical anatomy group have better results in many ways including learning interest, learning motivation, knowledge fastness, operation ability, clinical way of thinking, integration of anatomical and clinical knowledge, and communication skills etc. Conclusion The application of minimally invasive surgery in topographical anatomy teaching can fulfill the requirements of early contact of the minimally invasive surgery and related surgical appliances used in clinics for medical students, especially clinical medical students and can also facilitate anatomy teacher to understand the development of clinical surgery and teaching purpose, as well as enhance the communication between anatomy teaching and clinical practice.