Traditional Chinese Medicine (TCM) has been popular for thousand years in prevention and treatment of chronic diseases synergistically with Western medicine while producing mild healing effects and lower side effects. Although many TCMs have been proven effective by modern pharmacological studies and clinical trials, their bioactive constituents and the remedial mechanisms are still not well understood. Researchers have made great efforts to explore the real theory of TCM for many years with different strategies. Development of high performance liquid chromatography (HPLC) and mass spectrometry within recent decade can provide scientists with robust technologies for disclosing the mysterious mask of TCM. In this paper, important innovations of HPLC and mass spectrometry are reviewed in the application of TCM analysis from single compound identification to metabolomic strategy.