The roles of α-ketoglutarate (AKG) as a supplementary additive have been proved in improving the growth performance and immune response of several carps, while its effects are rarely studied on repairing oxidative damage in target organs of aquatic organisms in carbonate-alkaline environments, as well as the regulation of intestinal microbiota. As a prominent freshwater economic aquaculture species within the Chinese fishery industry, crucian carp (Carassius auratus) has good attributes of swift growth and robust adaptability, making it an ideal model for probing into the saline-alkaline adaptation mechanism of freshwater fishes. This study explored the mechanisms by which AKG modulates antioxidant enzymes, digestive enzymes, and intestinal microbiota in crucian carp under carbonate-alkaline stress. Using biochemical analysis and 16S rRNA sequencing, five experimental groups were established: a freshwater control group (group C), two carbonate-alkaline exposure groups (20 mmol/L NaHCO3, group T; 40 mmol/L NaHCO3, group F), and two AKG supplementation groups (20 mmol/L NaHCO3, group TA; 40 mmol/L NaHCO3, group FA). The experimental crucian carp were exposed to 20 and 40 mmol/L NaHCO3 for a period of 30 days. Finally, six biochemical indicators and intestinal microbiota of the experimental carps were measured and then analyzed with GraphPad Prism 9.0, principal co-ordinates analysis (PCoA), and linear discriminant analysis (LDA). The results showed that with increasing carbonate-alkaline concentration, the activities of superoxide dismutase (SOD) and catalase (CAT) significantly decreased, while malondialdehyde (MDA) content increased. Moreover, the activities of digestive enzymes (amylase, AMS; trypsin, CHY; lipase, LPS) in the intestine were also significantly declined. However, after the exogenous addition of AKG, both antioxidant and digestive enzyme activities were notably restored, and MDA content significantly decreased. As shown in PCoA, there were some differences in clustering degree between carbonate-alkaline exposure groups (groups T and F), AKG supplementation groups (groups F and FA) and control group (C). Compared with the group C, the abundance of Proteobacteria increased significantly in the groups T and F, while the abundance of Firmicutes decreased. The dominant genera in the groups T and F were Sphingomonas and Shewanellaceae, respectively. In contrast, in the AKG-supplemented groups (groups TA and FA), the abundance of Proteobacteria decreased substantially, and Firmicutes considerably increased. The dominant genus in the group TA shifted to Bacillus, while Shewanellaceae remained dominant in the group FA. According to KEGG function prediction, the functions of the intestinal microbiota were mainly involved in multiple physiological processes such as energy metabolism, amino acid metabolism, carbohydrate metabolism, nucleotide metabolism, signal transduction, lipid metabolism, replication and repair, immune system and immune disease. In summary, this study demonstrated that carbonate-alkaline exposure destroyed the antioxidant defense system in the intestine of crucian carp, leading to oxidative stress, while reducing the abundance of beneficial intestinal microbiota. AKG can enhance the antioxidant enzymes of crucian carp by neutralizing excess oxygen radicals and inhibiting lipid peroxidation. Owing to the improvement of the absorption and transport of nutrients, the digestive enzyme activity of crucian carp was intensified. Furthermore, AKG regulates the composition of beneficial intestinal flora by means of providing energy support. In conclusion, supplementing with AKG effectively alleviates the toxic effects of carbonate-alkaline environment.