Abstract:Widely targeted metabolomics was used to study the difference of metabolites content in the needles of Taxus wallichiana var. mairei and Taxus wallichiana var. mairei cv. ‘Jinxishan’. The results shoowed that: (1) a total of 689 metabolites and its integral quantitative value were found, including 326 primary metabolites, 334 secondary metabolites and 29 other components. (2) The results of quantitative analysis showed 71 metabolites content was significantly difference. Most of differential metabolites between T. mairei and T.‘Jinxishan’ were significant enriched in primary metabolic pathways, such as glycometabolism and lipid biosynthesis pathways, as well as secondary metabolic pathways such as flavonoids biosynthesis pathways. (3) A large number of metabolites in the amino acid and flavonoid biosynthesis pathway were significantly accumulated in T.‘Jinxishan’, while the differential metabolites in sugar metabolism, lipid synthesis and TCA cycle pathways were mainly accumulated in T.mairei. The study considered that the increase of flavonoid content was attributed to the co-regulation of phenylalanine and tyrosine metabolic pathways, which improved the adaptability of T.‘Jinxishan’ to the environment. At the same time, the energy was supplyed by synthesizing large amounts of amino acids to make up for the lack of energy ,caused by the decrease of metabolites content in glycometabolism, lipid biosynt hesis and TCA cycle pathways.