China contains vast areas of saline-alkali waters. Therefore, fish farming in such waters is crucial to ensuring domestic food supply and safety in the future and is also necessary for achieving the strategic goal of “expanding capacity, improving quality, and increasing efficiency” of China’s existing land area. The breeding of saline-tolerant fish species and the establishment of suitable breeding patterns are the key approaches to the efficient utilization of saline-alkali waters. The stability of key metabolic pathways in target organs is necessary for fish to adapt to changes in the external habitat. Gills are the salt-tolerant target organs of fish, and the effect of Rh glycoprotein on the ammonium transporter has been confirmed. However, uncertainty remains around the material basis and mechanism of regulation at the cellular level. This lack of understanding restricts the targeted breeding of salt-tolerant fish, which has become a key bottleneck requiring an urgent solution for the sustainable development of the saline-alkali fish industry. In this study, the saline-alkali tolerant Carassius auratus gibelio variety in China was used as the research object. Specimens were exposed to fresh water in the control group (Con), and three different concentrations of alkali in the stress groups: 20 mmol/L NaHCO₃ (CA20), 40 mmol/L NaHCO₃ (CA40), and 60 mmol/L NaHCO₃ (CA60). Metabolomics were used to screen for endogenous differential metabolites. Statistical analysis of metabolic pathways and multivariate data was used to explore the response mechanism of C. a. gibelio to alkali stress. The results showed that the gill tissue metabolites screened out 89 differential metabolites in the positive and negative ion mode, of which 50 were up-regulated and 39 were down-regulated, mainly enriched in glycerophospholipid metabolism, sphingolipid metabolism, arachidonic acid metabolism, and benzene Alanine metabolism, while the biosynthesis of phenylalanine, tyrosine, and tryptophan was represented by 12 metabolic pathways. This study shows that, after alkali stress, the glycerophospholipid in C. a. gibelio regulates the transport of substances inside and outside the cell membrane, and the pathway to synthesize sphingomyelin and sphingosine is inhibited. As the concentrations of prostaglandins, leukotrienes, and L-phenylalanine in the metabolites increase, the detoxification function increases and inflammatory response decreases. This metabolic mechanism may be a key reason for the tolerance of C. a. gibelio carp to alkali stress. This study explored the toxic effect and physiological regulation mechanism of alkali stress on crucian carp and provided a theoretical basis for further research into the breeding of excellent salt-tolerant fish species.