Abstract: In this study, metabolomics was used to identify and analyze the small molecule metabolites of Gastrodia elata before and after bolting, in order to understand the development process of Gastrodia elata tuber from the dormant stage to the bolting stage. Through LC-MS/MS detection, principal component, orthogonal partial least squares discrimination and path analysis, the results showed that 65 metabolites with significant differences were identified before and after bolting, including amino acids and their derivatives, organic acids and their derivatives, fatty acids and their derivatives, alkaloids, aromatics, nucleosides/amino acids, nucleosides, nucleotides, thiourea, sugars, terpenes, vitamins, steroids, steroid saponins and other 14 types of compounds, respectively, among which the up-regulated metabolites were mainly amino acids and their derivatives, alkaloids, etc., and the down-regulated metabolites were mainly were mainly fatty acids and their derivatives and organic acids and derivatives. KEGG analysis showed that the differential metabolites were mainly concentrated in the pathways related to benzoxazine biosynthesis, arginine and proline metabolism, and zeatin biosynthesis.