Objective To explore the effect of applying evidence-based medicine theory to quality management in long-term-system clinical medicine teaching. Methods We introduced the concept of evidence-based quality management system of clinical medicine to the delivery of teaching with Internet-based teaching quality real time supervision system as the core. A special quality scale was used to assess the teaching quality of teachers and the results were analyzed by SPSS 10.0 using u test. Results The system stored 853 280 pieces of data from the years 2001 to 2003. Up to 96.4% (275/285) of the evaluated topics scored over 85 points. Whether the teachers had overseas experience or not and whether their ages were over 45 or not had no significant influence on the teaching quality (P ＞0.05), but their degrees had influence on the teaching quality (P ＜0.05). Conclusion In long-term-system clinical medicine teaching quality management, we should apply the concept and approach of EBM to our practice so that we can ensure that the teaching quality of long-term-system clinical medicine will improve steadily.