The mud crab Scylla paramamosain is introduced to inland saline-alkaline water, but its survival is still a challenge. In this study, we performed a nuclear magnetic resonance-based metabolomic analysis of the gut of the mud crab during the saline-alkaline water pond culture and dietary supplementation with trimethylamine Noxide (TMAO), which was depleted in the gut, using a simulated saline-alkaline culture of the mud crab. We observed that the gut metabolite profile of mud crabs was significantly affected by saline-alkaline stress. Following a multivariate data analysis, we identified significantly changed metabolites associated with salinealkaline stress such as the depleted succinate, trimethylamine, and TMAO as well as the accumulated taurine, putrescine, and glucose, indicating a disruption in osmoregulation and energy metabolism. Importantly, dietary supplementation of 0.2 % TMAO promoted the survival of the mud crab in saline-alkaline water, and improved the activities of Na+/K+-ATPase, vacuolar-type ATPase, and carbonic anhydrase in the gill as well as transcriptional expressions of pk, hk, fbp, and pepck in the hepatopancreas, which suggests the vital role of TMAO in osmoregulation, acid-base homeostasis, and glucose metabolism. These findings provide a potential alternative of feed additive for the mud crab cultured in saline-alkaline water.