The application of chromatography, a modern technology for highly efficient separation and analysis in the research of therapeutic basis matter and quality control of traditional chinese medicine (TCM), is summarized. A new strategy with metabonomics is put forward to achieve integral study on therapeutic basis matter and action mechanism of TCM, and to reveal and control the comprehensive quality of TCM. Modern chromatography and hyphenated techniques are one of the important technique platforms in quality control of TCM.