The changes in quality indices (pH, acidity, protein, fat, and lactose) of yak, cattle-yak, and cow milk were analyzed during cold storage at 4 °C. The effects of cold storage time on volatile compounds of three kinds of raw milk were compared and the potential volatile compounds associated with raw milk deterioration were screened by headspace–gas chromatography–ion mobility spectrometry (HS-GC-IMS) and principal component analysis (PCA). During the whole refrigeration process, yak milk showed more obvious changes in pH and acidity than cow milk and cattle-yak milk, the change was more significant in the later stage of refrigeration (p < 0.05). And the contents of fat, protein, and lactose in yak milk changed significantly after 1 d of cold storage (p < 0.05). In total, 35 volatile components (including ketones, esters, aldehydes, alcohols, and others) were identified in the three raw milk samples during cold storage, including 13 common compounds. Their contents were higher in yak milk than in cattle-yak and cow milk. The contents of 2-ethyl-5-methylpyrazine, 2-pentanone, pyridine, 2-butanone, n-butyraldehyde, and 2,3-butanedione showed a gradual increase with the increase in cold storage time in three kinds of raw milk. These results can be used as monitoring markers of raw milk freshness.