【Objective】 Astragalus membranaceus (Fisch.) Bge. var.mongholicus (Bge.) Hsiao is an important primitive plant of Astragali radix, and its main planting areas are arid and semi-arid areas in Inner Mongolia, Shanxi, Gansu and other places, and irregular intermittent rainfall causes the plant drought and rehydration cycle. Studying the characteristics of metabolites in A. membranaceus var. mongholicus during drought and rehydration is crucial to understand the drought stress mechanism in response to natural intermittent rainfall.【Methods】 In this experiment, the seedlings of annual A. membranaceus var. mongholicus were used as materials, subjected to repeated drought stress and rehydration treatment, measured soil nutrients and their root length and root diameter in potted plants, and analyzed the primary differential metabolites of A. membranaceus var. mongholicus using NMR based metabolomics technology, And conduct differential metabolite screening and metabolic pathway analysis; The content of total flavonoids, total saponins, and polysaccharides in the roots of A. membranaceus var. mongholicus under repeated drought stress treatment was determined using sodium nitrite aluminum nitrate sodium hydroxide method, vanillin acetic acid colorimetry, and phenol sulfuric acid colorimetry. 【Results】 The results showed that (1) A. membranaceus var. mongholicus showed a trend of decreasing root diameter and increasing root length and fibrous root density when facing drought stress. (2) Under drought and rehydration treatment, a total of 42 metabolites were detected in the metabolome, mainly amino acids and their derivatives, organic acids, amines, ammonia compounds, and sugars; Metabolic pathway analysis found that plants mainly affect their amino acid metabolism pathways during repeated drought stress. By increasing the content of aspartate, alanine, glutamate, proline, and arginine, and reducing the content of asparagine, tryptophan, and 4-Aminobutyrate, they enhance their drought resistance. Specifically, the increase in metabolites such as alanine, glutamate, and proline is about 1～3 times greater, Metabolites such as tryptophan and 4-aminobutyric acid decreased by about 1-2 times. (3) Under the first round of drought stress, the accumulation of total saponins in Astragalus membranaceus decreased, while after the second round of drought stress, the production of three active substances, namely saponins, total flavonoids, and polysaccharides, all showed a downward trend. 【Conclusion】 The results of this study indicate that amino acids and their derivatives are closely related to the mechanism of A. membranaceus var. mongholicus in response to water stress, and the plant itself also regulates its secondary metabolites in response to environmental changes.