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Mammalian skeletal muscle is composed of various muscle fibers that exhibit different physiological and metabolic features. Muscle fiber type composition has significant influences on the meat quality of livestock. In this study, we comprehensively analyzed the whole transcriptome profiles of the oxidative muscle biceps femoris (BF) and the glycolytic muscle obliquus externus abdominis (OEA) of yak. A total of 1436 mRNAs, 1172 lncRNAs, and 218 circRNAs were differentially expressed in the oxidative muscles compared with the glycolytic muscles. KEGG annotation showed that differentially expressed mRNAs regulated by lncRNA and circRNA were mainly involved in PPAR signaling pathway, citrate cycle (TCA cycle), and PI3K-Akt signaling pathway, which reflect the different metabolic properties between oxidative and glycolytic muscles. In addition, regulatory networks associated with muscle fiber type conversion and mitochondria energy metabolism in muscles were constructed. Our study provides new evidence for a better understanding of the molecular mechanisms underlying skeletal muscle fiber determination and meat quality traits of yak. • We explored metabolic differences between oxidative and glycolytic skeletal muscles of yak. • Oxidative and glycolytic skeletal muscles showed distinct transcriptome profiles. • Numerous ncRNAs were closely related to distinct metabolic features between oxidative and glycolytic skeletal muscles. • Several signaling pathways related to skeletal muscle energy metabolism and meat quality traits were identified. • The result revealed possible candidate genes and ncRNAs for improvement of meat quality of yak. [ABSTRACT FROM AUTHOR]