Salinity is an important factor in the water environment, and salinity can cause changes in fish metabolism, which may be further reflected by changes in feed nutrient requirements. Methionine is one of the key components of feed nutrition. However, the methionine nutritional requirements and metabolism of Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) at different salinities are still unknown. The GIFT is a euryhaline fish, and a 60-day experimental trial was conducted to examine the interactive effects of salinity and dietary methionine levels (DMLs) on the growth performance and physiological responses of GIFT. A 6 × 2 factorial design was used to formulate six isonitrogenous and isoenergetic diets with six DMLs (0.38%, 0.53%, 0.76%, 0.92%, 1.12%, 1.30%) and two salinity levels (freshwater, 0 ppt; brackish water, 8 ppt). The results showed that DML significantly affected the growth performance and feed utilization of GIFT (4.25 ± 0.01 g), and the optimum growth performance and feed utilization efficiency were observed in freshwater and brackish water group at 0.76% and 0.92% DMLs, respectively. However, there was no significant difference in growth performance and feed utilization between the freshwater and brackish water cultures. In addition, there was a significant interaction between salinity and DMLs. Based on the SGR and FCR, the quadratic regression analysis showed that the optimal methionine requirements of juvenile GIFT were 0.75%, 0.77% (freshwater) and 0.79%, 0.82% (brackish water), respectively. In brackish water culture, GIFT showed higher levels of protein and lipid anabolism metabolism-related genes, while in freshwater culture, it showed higher mRNA levels of glucose metabolism and fatty β-oxidation genes. At both salinities, the appropriate level of methionine promoted protein synthesis and the pentose phosphate pathway of GIFT. Interestingly, in brackish water culture, high levels of glycolysis-, glycogen synthesis- and lipid synthesis metabolism-related genes were observed under excessive DML, while in freshwater culture, similar phenomena were observed when DML was relatively deficient. In conclusion, protein metabolism may be closely related to the adaptation of GIFT to salinity and the methionine requirement of juvenile GIFT cultured in brackish water (0.79–0.82%) was higher than that cultured in freshwater (0.75–0.77%), which may provide a theoretical foundation for the exploitation of formulated feed for GIFT cultured in brackish water.