To reveal the metabolite differences in mutton samples from different regions, specialty muttons from the Chaka, Yushu, and Qilian counties of Qinghai province, Sichuan, Inner Mongolia, and Ningxia were subjected to untargeted metabolomics analysis, using ultra-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UPLC-QTOF-MS), multivariate statistical analysis, and pathway analysis. Using the VIP≥1 and P<0.05 criteria, 176 differential metabolites, including amino acids, amino acid metabolites, benzene, substituted benzene derivatives, organic acids, organic acid derivatives, heterocyclic compounds, nucleotides, and nucleotide metabolites, were identified in muttons from Chaka, Yushu, and Qilian. Furthermore, 88 metabolic pathways, including the histidine metabolism, metabolic, D-glutamine and D-glutamate metabolic, and cofactor and amino acid biosynthesis pathways, were annotated. Using the VIP≥1, P<0.05, and FC≥2 or FC≤0.5 criteria, 50 differential metabolites, including amino acids, amino acid metabolites, glycerophospholipids, fatty acids, alcohols, amines, benzene, and substituted benzene derivatives, were identified in specialty muttons from the six regions. In all, 24 metabolic pathways, including metabolic, purine metabolism, tyrosine metabolism, ferroptosis, and arachidonic acid metabolism pathways, were annotated. Therefore, broad metabolite differences between mutton from different regions can be revealed using untargeted metabolomics analysis. The findings of this study have paved a path for the identification of specialty muttons from different regions and the assessment of their quality.