Evidence-based research is the essential method for the modernization of traditional medicine. China and Japan have made great progress in traditional Chinese medicine and Japanese Kampo medicine after years of evidence-based research, but there are also shortcomings. This paper compares the current situation of evidence-based research in traditional medicine from the aspects of the system of clinical evidence production and evaluation, standardization of clinical research report, standardization of traditional medicine in China and Japan, evaluation of the totality of clinical evidence via systematic review, application of clinical evidence via clinical practice guideline and development of research methodology. The purpose of this paper is to seek mutually complementary fields, and to provide enlightenment for future Chinese medicine and Japanese Kampo medicine evidence-based cooperation research.