The skeletal muscle fiber type is a key determinant of meat quality. However, the molecular mechanisms underlying the differences in flavor precursors between fast-twitch and slow-twitch muscles in mutton remain unclear. The gluteus medius (GM, glycolytic type) and semitendinosus (ST, oxidative type) muscles of Turpan black sheep are two representative skeletal muscles that differ markedly in muscle fiber types. In this study, amino acids, fatty acids, lipidomics, and proteomics were integrated to systematically compare the molecular differences between the GM and ST. The results showed that the ST muscle had significantly higher levels of umami amino acids (glutamic acid, Glu; aspartic acid, Asp) and the mutton-specific flavor contributor gondoic acid (C20:1n-9) than the GM, whereas the GM exhibited higher contents of sweet-tasting amino acids (alanine, Ala; proline, Pro). Lipidomics and proteomics analyses identified 389 differentially abundant lipids and 480 differentially expressed proteins. Combined analysis indicated that the differential molecules were mainly enriched in glycerophospholipid metabolism and pathways regulating lipolysis, which are the main metabolic networks influencing the accumulation of flavor precursors. In addition, phosphatidylethanolamine (PE), phosphatidylcholine (PC), cardiolipin (CL), C20:1n-9, hexokinase 2 (HK2), pyruvate kinase M (PKM), myosin heavy chain 7 (MYH7), and myosin heavy chain 2 (MYH2) were identified as the key candidate markers. Overall, these data provide new insights into the molecular mechanisms by which muscle fiber type affects mutton flavor quality and offer potential molecular targets for improving mutton flavor through genetic selection and nutritional regulation.