Metabolomics, a branch of systems biology, has gained extensive attention and profound achievements in the plant. Although plant metabolomics is to be explored, it has been one of the most effective methods to study the physiological and biochemical process and gene modification in pattern plants. We herein summarized the concept, development, and application of metabolomics and prospected the potentials in the metabolite profiling for plant. Metabolomics provides an omics' methodology to elucidate the whole biological process, identify and quantify the complex components in the plant. A number of metabolites present in the plant are active components of traditional Chinese medicine, and these bioactive components are influenced by the multi-factors such as environment, species, and processing methods etc. Therefore, it is of great importance to analyze a wide spectrum of compositions with diverse chemical characteristics and varied concentration, which is the foundation to quality control, allowing the elucidation of the pharmacological effectiveness, and further exploiting of traditional Chinese medicine.