Water temperature plays a crucial role in the growth, survival, and reproduction of fish species, as they make up the majority of aquatic fauna. In this study, the effects of low temperature were studied on the functional state of juvenile golden pompano (Trachinotus ovatus) under low-temperature stress. The study was conducted at 28°C in the control group and 18°C in the cold group for 14 d to determine the intestinal tissue, digestive and antioxidant enzyme activities, and metabolites of juvenile fish. The results showed that: (1) the swelling degree of the muscle layer deepened and was congested with a longer low-temperature stress period. The folds were sparse, from slight swelling to shedding and deformation. The intestinal mucosa was necrotic and had vacuoles, and the number gradually increased. Serious erosion of the villi occurred. (2) The specific activities of digestive enzymes showed a downward trend. (3) The intestinal superoxide dismutase (SOD) activity, malondialdehyde (MDA) content, and glutathione peroxidase (GSH-Px) activity showed an upward trend. The intestinal catalase (CAT) activity showed a downward trend. (4) Compared with the control group, there were 28 metabolites in the cold group showing significant differences, among which Z, 11Z, 14Z-eicosatrienoic acid, stearic acid, and adrenic acid showed an upward trend. In contrast, spermidine and uracil showed a downward trend. Among the enriched metabolic pathways, the main differential pathways were unsaturated fatty acid biosynthesis, fatty acid biosynthesis, linoleic acid metabolism, pyrimidine metabolism, and β-alanine metabolism. According to metabolomic analysis, under low-temperature stress, the fish body improved the synthesis of unsaturated fatty acids and saturated fatty acids to adapt to a low-temperature environment and consumed spermidine to improve its immune ability to clear the peroxide generated by the synthesis of unsaturated fatty acids in the body so that the cells were protected from oxidative damage. After 14 days, low-temperature stress affected metabolites and enzyme activity indices in juvenile golden pompano. Low-temperature stress causes changes in intestinal antioxidants and digestive enzymes and damage intestinal tissues. As a result of this exploration of how low temperatures affect the juvenile golden pompano, the foundation is laid for future studies, such as the molecular mechanisms of low-temperature adaptation in fish species.