Abstract: Low-temperature events constitute a major environmental challenge for warm-water groupers, affecting feeding, tissue integrity, and metabolic homeostasis and the physiological recovery after water temperature returns to a suitable range may involve processes distinct from those activated during low-temperature exposure. This study investigated changes in muscle histological structure, transcriptional profiles, and metabolism in juvenile Yunlong grouper (Epinephelus moara ♀ ×E. lanceolatus ♂) during low-temperature stress and subsequent rewarming. In the low-temperature-rewarming (LT-RW) group, water temperature decreased from 24℃ to (16±0.5)℃ within 10h and maintained at (16±0.5)℃ until day 7. After sampling on day 7, the temperature increased to (24±0.5)℃ within 10h and maintained at this level until day 14, while fish continuously kept at (24±0.5)℃ served as the control group. Results showed that the feeding rate was significantly lower than that of the control group starting from day 1 (P<0.05), and histological examination showed loosely arranged muscle fibers with widenedinter-fiber spaces and localized separation. A total of 5760 differentially expressed genes and 353 differential metabolites were identified in LT7 vs. CT7. These changes were mainly associated with the autophagy-proteasome system, extracellular matrix-related processes, membrane lipid metabolism, and glutathione-related metabolism, indicating prominent responses related to protein quality control, membrane lipid adjustment, and structural homeostasis during low-temperature exposure. After 7d of rewarming, the daily feeding rate increased and muscle histological structure improved relative to the low-temperature stage. However, the transcriptomic and metabolomic profiles of the RW7 group remained clearly distinguishable from those of the concurrent CT14 group, with 9557 differentially expressed genes and 532 differential metabolites identified in RW7 vs. CT14, mainly involving central carbon metabolism, oxidative phosphorylation, fatty acid metabolism, nucleotide metabolism, muscle cytoskeleton, and muscle contraction-related processes. RT-qPCR further demonstrated distinct expression trajectories between the two thermal stages. The autophagy- and proteasome-related genes ulk2, atg13, and psmd11a were significantly upregulated during the low-temperature stage but showed no significant differences from the concurrent control after rewarming. In contrast, pfkm-like shifted from significant upregulation during low-temperature exposure to significant downregulation during rewarming. Moreover, acadvl, ckm, ldha-like, mdh2, cox7a, and atp5b showed no significant changes during the low-temperature stage but were significantly downregulated after rewarming. Integrated analysis of the transcriptomic, metabolomic, and RT-qPCR results revealed different molecular response patterns between low-temperature exposure and rewarming, with the low-temperature stage characterized by upregulation of autophagy- and proteasome-related genes, extracellular matrix-associated structural alterations, and changes in metabolites related to membrane lipid and glutathione metabolism. After 7d of rewarming, the autophagy- and proteasome-related genes no longer differed significantly from control group, whereas representative genes involved in fatty acid β-oxidation, glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and muscle contraction were significantly downregulated, and muscle histological structure showed only partial recovery. These results indicate that rewarming is not simply a reversal of the low-temperature response but represents a distinct regulatory stage involving the readjustment of energy substrate utilization and muscle structure and function, providing multi-omics evidence for understanding low-temperature stress responses and rewarming adaptation in warm-water groupers and offering a theoretical basis for refining overwintering and post-cold-spell husbandry strategies in grouper aquaculture.