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It is well known that different muscles of yak exhibit distinctive characteristics, such as muscle fibers and metabolomic profiles. We hypothesized that different muscles could alter the flavor profile of yak jerky. Therefore, the objective of this study was to investigate the differences in flavor profiles of yak jerky produced by longissimus thoracis (LT), triceps brachii (TB) and biceps femoris (BF) through electronic nose (E-nose), electronic tongue (E-tongue), gas chromatography–mass spectrometry (GC-MS) and gas chromatography–ion mobility spectrometry (GC-IMS). The results indicated that different muscles played an important role on the flavor profile of yak jerky. And E-nose and E-tongue could effectively discriminate between yak jerky produced by LT, TB and BF from aroma and taste points of view, respectively. In particular, the LT group exhibited significantly higher response values for ANS (sweetness) and NMS (umami) compared to the BF and TB groups. A total of 65 and 47 volatile compounds were characterized in yak jerky by GC-MS and GC-IMS, respectively. A principal component analysis (PCA) model and robust principal component analysis (rPCA) model could effectively discriminate between the aroma profiles of the LT, TB and BF groups. Ten molecules could be considered potential markers for yak jerky produced by different muscles, filtered based on the criteria of relative odor activity values (ROAV) > 1, p < 0.05, and VIP > 1, namely 1-octen-3-ol, eucalyptol, isovaleraldehyde, 3-carene, D-limonene, γ-terpinene, hexanal-D, hexanal-M, 3-hydroxy-2-butanone-M and ethyl formate. Sensory evaluation demonstrated that the yak jerky produced by LT exhibited superior quality in comparison to that produced by BF and TB, mainly pertaining to lower levels of tenderness and higher color, taste and aroma levels. This study could help to understand the specific contribution of different muscles to the aroma profile of yak jerky and provide a scientific basis for improving the quality of yak jerky.