The metabolomic profiles of raw camel milk (RCM), heated camel milk (HCM) and camel milk powder (CMP) were analysed by ultra-high-performance liquid chromatography coupled with quadrupole time of flight mass spectrometer (UHPLC-Q-TOF/MS). One hundred and nineteen significantly changed metabolites with variable importance for the projection (VIP) > 1 (t-test p < 0.05) from the positive mode were selected and identified in RCM, HCM and CMP. These metabolites included saccharides, glycosylamines, adenosines, and phospholipid. Among the saccharides, the content of d-lactose was the highest and slightly increased after thermal treatment. Dipeptides, including His–Pro and Lys–Trp, were significantly increased in HCM and CMP. As for glycosylamines, the content of N-acetylneuraminic acid was the highest. The amounts of larixinic acid increased dramatically in HCM and CMP (p < 0.001), which may improve the flavour of camel milk.