Camel milk produces many beneficial functional compounds and affects body health through metabolism. The differential metabolites of bactrain camel milk in Alxa before and after fermentation were identified by liquid chromatography-tandem mass spectrometry based metabolomics (LC-MS/MS). The differential metabolite pathway types were also identified in this paper. We obtained the following results that 148 and 82 differential metabolites were detected in positive and negative ion mode respectively, 85 differential metabolites were shown a significant upward trend and 63 with downward trend after fermentation in positive ion mode. Meanwhile, 32 differential metabolites characterized upward trend and 50 characterized downward trend in negative ion mode. The differential metabolites were mainly organic acids, amino acids, esters, vitamins and other substances contained in camel milk. Among them, most up-regulated substances had the functions of lowering blood pressure, lowering blood sugar, treatment of inflammation, antibiosis and other effects. Many harmful substances were significantly down-regulated after camel milk fermentation. However, there were also some metabolites whose prebiotic functions have been weakened by camel milk fermentation, which may provide reference values for healthcare function, exploitation and application of camel milk.