Abstract: This experiment aimed to investigate the differences in metabolites of different varieties from Xinjiang sea buckthorn, ultra high performance liquid chromatography-mass spectrometry (UPLC-QTOF-MS) coupled with multivariate statistical analysis and pathway enrichment analysis were used to characterize the metabolites of six Xinjiang sea buckthorn species ('Mixed Fruit', 'Giant', 'Shenqunhon', 'Wucifeng', 'Xiangyang' and 'Zhuangyuan Yellow') were subjected to non-targeted metabolomics study. The results showed that a total of 334 metabolites were obtained from the metabolomic analysis. Based on Log₂FC absolute value ≥1 and FDR<0.05 analysis, a total of 112 differential metabolites were screened between 'Mixed Fruit' and 'Giant'; 'Mixed Fruit' and 'Shenqunhon' screened a total of 118 differential metabolites between 'Mixed Fruit' and 'Wucifeng'; 'Mixed Fruit' and 'Wucifeng' screened a total of 67 differential metabolites; 'Mixed Fruit' and 'Wucifeng' screened a total of 67 differential metabolites between 'Mixed Fruit' A total of 160 differential metabolites were screened between 'Mixed Fruit' and 'Xiangyang'; and a total of 126 differential metabolites were screened between 'Mixed Fruit' and 'Zhuangyuan Yellow''. The metabolic pathway enrichment analysis showed that the differential metabolites of different large-fruited sea buckthorns were mainly enriched in the pathways of unsaturated fatty acid biosynthesis, fatty acid biosynthesis, tryptophan metabolism, and flavonoid and flavonol biosynthesis. Based on the VIP value >1, Log₂FC absolute value ≥1 and FDR<0.05 screening criteria, a total of five differential metabolites were found, and overall high abundance and lipid-like molecules, phenylpropanes and polyketides were found in sea buckthorn, ranging from 38% to 81% and 15% to 49%, respectively, among which erucic acid amide, linoleic acid, palmitic acid, narcissin, isorhamnetin-3-O-glucoside, rutin, etc. may be the key metabolites to identify different Xinjiang sea buckthorn. Non-targeted metabolomics can elucidate the metabolic differences of different varieties of Xinjiang sea buckthorn at the overall level, which provides scientific basis for the selection and breeding of Xinjiang sea buckthorn varieties and their processing and utilization.