Conservation and utilization of Brachymystax tsinlingensis Li, 1966 (B. tsinlingensis), an endangered cold-water fish, is severely hampered by heat stress. In this study, heat stress and recovery experiments were firstly performed and implied that the intestine of B. tsinlingensis remained capable of self-regulation under heat stress. Therefore, transcriptome analysis was used to investigate the homeostatic mechanisms of B. tsinlingensis during temperature fluctuations. The results showed that a total of 5775 differentially expressed genes (DEGs) (1725 up- and 4050 down-regulated) were identified in the heat stress group, and 4312 DEGs (2024 up- and 2228 down-regulated) were identified in the recovery group when compared to their expression levels in the control group. Through Gene Set Enrichment Analysis (GSEA), citrate cycle (TCA cycle), oxidative phosphorylation, apoptosis, ferroptosis, focal adhesion, and tight junction pathways were found to be significantly up-regulated during heat stress, and declined during the recovery process. The results illustrated that heat stress caused ferroptosis and apoptosis in B. tsinlingensis. However, the organism was able to maintain homeostasis during temperature fluctuations modulating its energy metabolism, as well as the barrier and immune functions of the intestine. These findings help to enhance our understanding of the acclimation mechanisms of cold-water fish in present-day climate change.