Abstract: To elucidate the response mechanisms of Scatophagus argus to carbonate alkalinity stress, we established a control group in freshwater and an experimental group exposed to 30 mmol/L carbonate alkalinity. Liver and gill tissues were collected at 0, 3, 6, and 9 hours post-stress for histological examination and transcriptome sequencing. Histological analysis revealed that under alkaline stress, liver cells exhibited varying degrees of atrophy and vacuolization, while gill tissues demonstrated damage characterized by epithelial cell shedding, gill lamella deformation, and larger spacing. Transcriptome sequencing after 9 hours of alkaline stress identified 270 differentially expressed genes (DEGs) in liver tissue, with 190 genes up-regulated and 80 down-regulated. These DEGs were primarily associated with pathways related to energy synthesis and metabolism, including cytochrome P450-related metabolism, adipocytokine signaling, and steroid metabolism. Notably, the up-regulation of hsp70 and hbb1, alongside the down-regulation of gpx1, indicated the activation of oxidative stress response mechanisms. In gill tissue, 114 DEGs were identified, with 39 up-regulated and 75 down-regulated, affecting pathways such as cell adhesion, steroid biosynthesis, and PPAR signaling. The significant down-regulation of prkca and rab5a suggested a potential compromise in cell adhesion capacity. In addition, the common differentially expressed genes ck and nlrp12 in liver and gill tissues play a key role in immune defense. These findings indicate that the adaptation of S. argus to carbonate alkalinity stress involves structural and functional alterations in liver and gill tissues, along with the regulation of gene expression related to energy balance and immune response. This study provides critical insights into the molecular mechanisms underlying alkali resistance in S. argus.