<p>Gills, as crucial respiratory organs in fish, are extremely sensitive to temperature fluctuations in aquatic environments. However, the adaptive mechanism of largemouth bass (<i>Micropterus salmoides</i>) to low-temperature stress remains largely unknown. We investigated the effects of low temperature (10 ℃) on the largemouth bass gills at 0 (C), 2 (T0), 24 (T1), 48 (T2), 96 (T4), and 144 (T6) h post-exposure, subjecting tissues to histological analysis and transcriptome sequencing. Compared to the control group (25 ℃), the low-temperature groups showed 123, 3416, 4745, 4576, and 4615 differentially expressed genes (DEGs) at T0 vs. C, T1 vs. C, T2 vs. C, T4 vs. C, and T6 vs. C, respectively. The lipid metabolism, apoptosis, and immune response signaling pathways were significantly enriched based on the KEGG enrichment pathway analysis. Five low-temperature–specific modules were significantly correlated with low-temperature stress through weighted gene co-expression network analysis (WGCNA). Western blot (WB) analysis confirmed the upregulated expression of the HSP70 protein in gill tissues under cold stress, indicating its critical role in cold adaptation. Histological observations revealed structural disorganization, disordered cell arrangement, and compromised functional integrity in the gills of fish exposed to low-temperature treatment. In our study, <i>cirbpb</i> and <i>hmgb1</i> were identified for the first time in largemouth bass under low-temperature stress. Furthermore, <i>sik3</i> was discovered to play a functional role in low-temperature adaptation in fish, representing its first reported involvement in this process within teleosts. This study provides novel insights into the molecular mechanisms underlying gill responses to low temperature in largemouth bass and establishes a theoretical foundation for breeding cold-tolerant fish species.</p>