For the complexity of the metabolic pathways and the characteristics of “multiple components, multiple targets and the overall adjustment functions” of Traditional Chinese medicine (TCM) and natural products in organism, nowadays, metabonomics have been widely applied in TCM metabolites and pharmacodynamic mechanism researches. However, the study of metabonomics needs much exogenous and endogenous metabolites information of biological fluids, which requires more powerful analytical techniques. The paper reviewed liquid chromatography coupled with mass spectrometry (LC-MS) techniques commonly applied to TCM metabolites and metabonomics researches. And then we summarized and comparatively analyzed the data of 23 literatures searched from Pubmed database. The advantages and disadvantages of different kinds of LC-MS techniques in TCM metabonomics studies were discussed, and the advantages of UPLC-Q-TOF/MS were indicated, which contributes to provide new ideas for TCM metabonomics researches.