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Simple Summary: Myostatin (MSTN) negatively regulates skeletal muscle growth. Although the role of MSTN in muscle hypertrophy can be investigated in depth, studies of MSTN in mitochondrial energy metabolism in muscle would be valuable. In this study, we evaluated the importance of MSTN in regulating mitochondrial energy metabolism in MSTN-knockout (Mstn−/−) mice and explored the possible mechanisms. A loss of MSTN inhibits oxidative phosphorylation, alters TCA cycle activity, and impairs ATP production in skeletal muscles. These changes may be achieved through TGF-β-Smad2/3. These results suggest that MSTN may be an important regulator of mitochondrial energy homeostasis in mice. Myostatin (MSTN) is an important negative regulator of skeletal muscle growth in animals. A lack of MSTN promotes lipolysis and glucose metabolism but inhibits oxidative phosphorylation (OXPHOS). Here, we aimed to investigate the possible mechanism of MSTN regulating the mitochondrial energy homeostasis of skeletal muscle. To this end, MSTN knockout mice were generated by the CRISPR/Cas9 technique. Expectedly, the MSTN null (Mstn−/−) mouse has a hypermuscular phenotype. The muscle metabolism of the Mstn−/− mice was detected by an enzyme-linked immunosorbent assay, indirect calorimetry, ChIP-qPCR, and RT-qPCR. The resting metabolic rate and body temperature of the Mstn−/− mice were significantly reduced. The loss of MSTN not only significantly inhibited the production of ATP by OXPHOS and decreased the activity of respiratory chain complexes, but also inhibited key rate-limiting enzymes related to the TCA cycle and significantly reduced the ratio of NADH/NAD+ in the Mstn−/− mice, which then greatly reduced the total amount of ATP. Further ChIP-qPCR results confirmed that the lack of MSTN inhibited both the TCA cycle and OXPHOS, resulting in decreased ATP production. The reason may be that Smad2/3 is not sufficiently bound to the promoter region of the rate-limiting enzymes Idh2 and Idh3a of the TCA cycle, thus affecting their transcription. [ABSTRACT FROM AUTHOR]