To investigate the impact of Isalo scorpion cytotoxic peptide (IsCT) on the immune function of immune organ (head kidney, spleen, and skin) of grass carp (Ctenopharyngodon idella), 540 fish (136.88 ± 0.72 g) were supplied with a different amount of IsCT (0, 0.6, 1.2, 1.8, 2.4, and 3.0 mg/kg diet) through a period of 60 days. Afterward, 24 fish were randomly selected from each group and were inoculated with Aeromonas hydrophila for a period of 6 days. Our findings suggested that appropriate IsCT complementation: (1) attenuated skin morbidity and histopathological structural changes in the head kidney and spleen (p < 0.05), which ensured the structural integrity of the immune organs; (2) increased the activity and expression of immune substances (p < 0.05), which in turn increased the function of the immune organs, promoting immune responses; (3) through the regulation of the Janus kinase/signal transducers and activators of transcription (JAKs/STATs) signaling pathway, the mRNA expression of anti‐inflammatory cytokines increased and the mRNA expression of pro‐inflammatory cytokines decreased, which in turn increased the function of the immune organs, reducing the inflammatory response (p < 0.05). However, the addition of IsCT did not affect the expression of IL‐12p35, STAT2, and STAT3a in the immune organ. Ultimately, this study provided evidence that IsCT enhanced immune function via the JAKs/STATs signaling pathway in the immune organ in grass carp after challenged with Aeromonas hydrophila.