Abstract: Traditional Chinese prescription is the main form of clinical medication of traditional Chinese medicine (TCM), and also the important carrier of TCM inheritance and innovation. Because of the bottle-neck problems such as unclear chemical basis, unclear function mechanism, unstable quality control and lack of evidence-based medicine, traditional Chinese prescription has been questioned frequently. It is difficult for traditional Chinese prescription to gain international approval, and its clinical application and industrial development are very limited. How to carry out the basic research of traditional Chinese prescription scientifically and effectively for better clinical application has become an urgent problem to be solved in the development of TCM. In recent years, the rising and developing of translational medicine has brought new opportunities and ideas for the innovation and development of TCM. This paper briefly described the difficulties in the clinical application and development of traditional Chinese prescription, discussed the present situation and the main problems in the translational research of TCM, and further condensed the research ideas and methods, with the purpose to provide beneficial guidance for the further research of TCM.