Metabolomics reflects the physiological states of organisms exposed to distinct environmental stimuli. However, little is known about the metabolic signatures of rainbow trout under different temperatures. In the present study, a 56-day experiment was conducted to evaluate the growth performance and metabolic signatures of liver tissues in rainbow trout (Oncorhynchus mykiss) juveniles exposed to seawater at 7 °C (T7), 11 °C (T11), 15 °C (T15) and 19 °C (T19), nearly covering the temperature ranges in aquaculture industry during different seasons. The results indicated that individuals cultured at 15 °C showed growth performance with significantly higher final weight, weight gain, and specific growth rate than the others. Furthermore, a total of 24 liver samples (6 replicated samples × 4 treatment groups) were performed for non-targeted metabolomics analysis, resulting in 4852 and 5688 effective ions detected by ESI+ and ESI− modes, respectively. Of them, 474 and 425 metabolites were systematically identified and annotated in ESI+ and ESI− modes, respectively. Nearly half of metabolites (43.94%, 395) were classified as lipids and lipid-like molecules in HMDB database. Based on the strict thresholds, a total of 150, 66 and 45 differential metabolites (DMs) were determined in three different comparisons, including T7 vs. T15, T11 vs. T15 and T19 vs. T15. It was noted that these DMs could be further grouped into 4 clusters according to their abundance tendencies as temperatures increased from 7 °C to 19 °C. The relative abundance of DMs associated with sphingolipid metabolism was continuously increased with the elevated temperatures, while a decreasing tendency was observed in these DMs related to glycerophospholipid metabolism. Meanwhile, DMs in phenylalanine and histidine metabolism displayed the highest abundance at 15 °C, and N-acyl taurine and vitamin metabolism was induced by high temperature (19 °C). Taken together, different temperatures strongly affected both amino acid and lipid metabolism in liver tissues of rainbow trout. The study provides insight into the potential physiological basis for the better cultivation and fisheries management of rainbow trout at different temperatures.