Climate change and intensified human activities have accelerated the salinization and alkalinization of aquatic environments, further shrinking the space for freshwater aquaculture. One of the key survival mechanisms for fish in saline-alkaline habitats is the conversion of accumulated endogenous ammonia into less toxic glutamine. This study focuses on the freshwater teleost, crucian carp (Carassius auratus), using the liver as the target organ. Three groups were established: 0, 20, and 40 mmol/L NaHCO3 stress groups. After 30 days, methionine sulfoximine was injected to block the glutamate pathway, respectively. Through a combination of biochemical analysis and metabolomics, this study investigated the mechanisms by which blocking the glutamate pathway under different NaHCO3 stress concentrations affects metabolism in the liver of crucian carp. Biochemical results indicated that saline-alkaline stress led to oxidative stress and impaired ammonia excretion in crucian carp, and these effects were exacerbated after blocking the glutamate pathway. Metabolomic results revealed significant alterations in pathways such as glycerophospholipid metabolism, arachidonic acid metabolism, and purine metabolism. The study demonstrates that blocking the glutamate pathway exacerbates lipid and energy metabolism disorders under saline-alkaline stress, with crucian carp compensating by regulating glucose metabolism to mitigate energy deficiencies. In summary, this study elucidates the metabolic changes in crucian carp following the blockade of glutamate pathway under carbonate-alkaline stress, providing insight into the mechanisms leading to liver inflammation and metabolic dysregulation, and offers preliminary insights into the effects on ammonia excretion, which lay a scientific foundation for future research on freshwater teleosts in saline-alkaline environments.