It is critical to investigate the adaptive development and the physiological mechanism of fish in external stimulation. In this study, the response of Barbus capito to salinity–alkalinity exposure was explored by high‐throughput nontargeted and liquid chromatography–mass spectrometry‐based metabolomics to investigate metabolic biomarker and pathway changes. Meanwhile, the biochemical indexes of Barbus capito were measured to discover the chronic impairment response to salinity–alkalinity exposures. A total of 29 tissue metabolites were determined to deciphering the endogenous metabolic changes of fishes during the different concentration salinity–alkalinity exposures environment, which were mainly involved in the key metabolism including the phenylalanine, tyrosine, and tryptophan biosynthesis, arachidonic acid metabolism, pyruvate metabolism, citrate cycle, and glycerophospholipid metabolism. Finally, we found the amino acid metabolism as key target was associated with the endogenous metabolites and metabolic pathways of Barbus capito to salinity–alkalinity exposures. In conclusion, metabolomics is a potentially powerful tool to reveal the mechanism information of fish in various exposure environments.