Flavor is one of the most important sensory characteristics of meat. The development of taste and aroma can be attributed to thousands of flavor molecules and precursors that are present in meat tissues. As a result, the identification of these flavor compounds and an improved understanding of their roles are necessary for improving the sensory quality and customer appeal of meat products. In the current study, we compared the metabolic profiles of meat specimens from the Lubei white goats (LBB), Boer goats (BE) and Jining grey goats (JNQ) by untargeted liquid chromatography-mass spectrometry. Our metabolomic data revealed that the three types of goat meat showed significantly different profiles of fatty acids, aldehydes, ketones, lactones, alkaloids, flavonoids, phenolics and drug residues, which could underpin the nuances of their flavors. Taken together, our results provided insights into the molecular basis for sensory variations between different goat meat products.