Abstract: Plant metabolomics helps to illustrate the mechanisms underlying plant responses to environment change or gene mutations at the level of metabolites. Liquid chromatography-mass spectrometry (LC-MS) is characteristic of high resolution power and high sensitivity. Furthermore， LC-MS is suitable for the analysis of metabolites with high boiling point or high molecular weight or metabolites that are not thermostable. Based on these advantages，LC-MS analysis plays an important role in plant metabolomics. LC-MS has been significantly improved in several aspects in recent years， including fast LC-MS， nano LC-MS， 2D LC-MS， derivatization LC-MS etc. With the development of LC-MS technology， plant metabolomics has been successfully applied in many fields， including phenotypic discrimination， safety assessment of transgenic plants， biotic or abiotic stress study， identification of plant gene function， crop breeding etc.