This study employed non-targeted metabolomics based on liquid chromatography-mass spectrometry (LC-MS) to analyze the differences in metabolites between camel milk and cow milk. Junggar bactrian camel milk and cow milk from the same pastoral area were collected for analysis of small-molecule metabolites. Multivariate statistical analysis methods including principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were used in combination with the R language and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database for differential analysis. The results showed that a total of 984 metabolites were detected (572 and 412 in the positive and negative ion modes, respectively), the major ones being undefined metabolites, lipids and lipid-like molecules, and organic acids and their derivatives, which accounted for 30.39%, 27.13%, and 11.59% of the total number, respectively. Significant differences (P < 0.05) in small-molecule metabolites were found between camel and cow milk. Altogether, 67 differential metabolites predominated in camel milk, and 63 in cow milk. Compared with cow milk, the differential metabolic pathways in camel milk were primarily enriched in purine metabolism, phenylalanine metabolism, nicotinate and nicotinamide metabolism, vitamin digestion and absorption. These findings provide a scientific basis for the development of functional foods based on camel milk
