It is known that the marine euryhaline crab, mud crab (Scylla paramamosain), is capable of adapting to low salinity conditions through an innate osmoregulatory system. However, the influence of nutritional conditions during low salinity adaptation has not been fully elucidated. In this study, transcriptome analysis was employed to examine whether low salinity affects the AMP-activated protein kinase (Ampk) signaling pathway, and thereby carbohydrate and lipid metabolism. Further analysis revealed that low salinity activated the expression of P-Ampk and promoted glycolysis and lipolysis, which enhances glycogen and lipid utilization. Nutritional deprivation confirmed that nutrients influenced the survival and osmotic pressure regulation of mud crab under to low salinity via the Ampk signaling pathway. During adaptation to low salinity, carbohydrates were the primary energy source in the initial 7 days, followed by lipids. Further investigation showed that pharmacological stimulation of mechanistic targets in the Ampk signaling pathway using metformin could promote the osmotic pressure regulation of mud crab, confirmed the pivotal role of this pathway in low salinity adaptation. Overall, the present study demonstrated that nutrition, metabolism and osmotic pressure regulation interactively contribute to salinity adaptation in mud crab. Specifically, low salinity induced remodeling of nutritional metabolism homeostasis and promoted glycolipid catabolism, thereby providing energy for osmotic pressure regulation in mud crabs.