In order to know the possibility of producing medicinal components from hairy roots of Ammopiptanthus mongolicus,UHPLC-Q-TOF-MS method combined with multivariate statistical analysis was used to analyze the chemical components of hairy roots and roots of A. mongolicus,PCA and OPLS-DA were used for data processing.The results showed that 3 982 and 4 209 metabolites were obtained from the hairy roots and roots of A. mongolicus at positive and negative ion modes,respectively,with 1 706 and 1 639 differential metabolites,among which 1 455 and 1 095 were up-regulated;there were 171 and 134 differential metabolites annotated to KEGG,which were enriched to 65 metabolic pathways,mainly concentrated in amino acid metabolism,secondary metabolites biosynthesis,carbohydrate metabolism,lipid metabolism,cofactors and vitamins metabolism,terpenes and polyketides metabolism,energy metabolism and nucleotide metabolism.The differential metabolites were mainly concentrated in amino acid metabolism and secondary metabolites biosynthesis,37.4% and 32.7% of the differential metabolites at positive ion mode,28.4% and 26.1% of the differential metabolites at negative ion mode.There were 11 pathways involved in the secondary metabolites biosynthesis,including flavone/flavonoid biosynthesis,alkaloid biosynthesis,β-lactam biosynthesis,glucosinolate biosynthesis,phenylpropanoid metabolism,etc.and the flavone/flavonoid biosynthesis pathway involved the most differential metabolites,accounting for 34% of the differential secondary metabolites,followed by the differential metabolites related to alkaloid biosynthesis,accounting for 24%.88.2% of differential metabolites in flavone/flavonoid biosynthesis pathway were up-regulated.The results of this study provide a theoretical basis for the accumulation and pathway elucidation of metabolites in hairy roots of A. mongolicus.