Cortisol can impact the transcription of downstream inflammation and immune-related genes via the glucocorticoid receptor (GR), thereby influencing the immune response and maintaining the homeostatic balance of the host. However, there is a lack of research on the mechanisms by which cortisol affects the immune response of Siberian sturgeon (Acipenser baerii) through GR. In this study, an anti-inflammatory state of Siberian sturgeon was established by the combined treatment of head kidney (HK) leukocytes with LPS + cortisol. Subsequently, the inflammation-related genes of the AbGR antagonistic group (LPS + cortisol + RU-486) and the AbGR non-antagonistic group (LPS + cortisol) were compared by qRT-PCR and high-throughput sequencing methods. Furthermore, an AP-1 agonist ASLAN003 was used to detect the regulatory effect of the AP-1 gene on inflammatory cytokines. The results showed that cortisol downregulated the expressions of il-1β, il-6, il-8, tnf-α, and il-17c that were induced by LPS, while simultaneously promoting the expressions of tgf-β1. Moreover, this pattern was reversed by adding RU486. When analyzing the differentially expressed genes in the transcriptome sequencing of HK leukocytes in AbGR antagonistic group, 261 significantly down-regulated genes and 194 significantly up-regulated genes were annotated. Furthermore, 26 differentially expressed genes related to inflammation in AbGR antagonistic group were enriched, and the key nuclear transcription factor AP-1 for regulating inflammation function of AbGR was selected based on the enrichment factor and p-value for subsequent research. In the HK leukocytes after cortisol + ASLAN003 treatment, the expressions of fosl1 and jund that were induced by ASLAN003 were significantly down-regulated after cortisol treatment. In this situation, the expression of tgf-β1 was significantly increased, and the expression of tnf-α was significantly decreased after cortisol treatment. Therefore, this study demonstrated that cortisol inhibits the expression of AP-1 through GR in Siberian sturgeon, and then regulates the generation of the inflammatory response.