Bats are the only mammals that fly and hibernate. Little is known about their overall metabolism in the brain during hibernation. In this study, brain proteins of torpid and active Myotis ricketti bats were fractionated and compared using a proteomic approach. Results showed that 21% (23 proteins) of identified proteins with significant expression changes were associated with amino acid metabolism and proteostasis. The expression levels of proteins involved in energy metabolism (15 proteins), cytoskeletal structure (18 proteins), and stress response (13 proteins) were also significantly altered in torpid bats. Over 30% (34 proteins) of differentially expressed proteins were associated with mitochondrial functions. Various post-translational modifications (PTMs) on PDHB, DLD, and ARG1 were detected, suggesting that bats use PTMs to regulate protein functions during torpor. Antioxidation and stress responses in torpid bats were similar to those of hibernated squirrels, suggesting a common strategy adopted by small hibernators against brain dysfunction. Since many amino acids that metabolize in mitochondria modulate neuronal transmissions, results of this study reveal pivotal roles of mitochondria in neural communication, metabolic regulation, and brain cell survival during bat hibernation. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Biological significance: This study reveals the mechanisms used by bats to regulate brain activities during torpor. These mechanisms include post-translational modifications and differential expression of proteins involved in mitochondrial electron transport, anaerobic glycolysis, TCA cycle efflux, cytoskeletal plasticity, amino acid metabolism, vesicle structure, antioxidation defense, stress response, and proteostasis. Our study provides insights in metabolic regulation of flying mammals during torpor and common strategies used by small hibernators in response to hibernation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.