Abstract: In order to explore the differences of metabolites between different Jiaosu samples, ultra-high performance liquid chromatography coupled to quadrupole time of flight mass spectrometry was used to identify and analyze the differential metabolites of blueberry jiaosu and sea-buckthorn jiaosu with metabolomics method. The results showed that 9 key metabolic differences in the two jiaosu samples. The comparative analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database indicated that the high metabolites enrichment and high significance involved six metabolic pathways, which were flavonoid and flavonol biosynthesis, pantothenic acid and coenzyme A biosynthesis, tyrosine metabolism, alanine, aspartic acid and glutamate metabolism, proline and arginine metabolism, and glutathione metabolism. According to the non-targeted metabolome analysis, this research initially revealed the differences in the metabolites of blueberry jiaosu and sea-buckthorn jiaosu. Accordingly, a theoretical reference has been presented for the study of function of fruit jiaosu.