Bacterial septicemia caused by Aeromonas hydrophila is one of the common bacterial diseases in aquaculture. Antimicrobial peptides, including hepcidin, are key components of the innate immune system in fish, playing a role in defense against pathogens. This study investigated the defense patterns of hepcidin in mandarin fish (Siniperca chuatsi) following A. hydrophila infection using gene expression analysis and in vitro antibacterial assays. We measured changes in the expression of iron metabolism-related genes (hepcidin, fpn, ftn, tf, tfr1) and immune-related genes (il-1β, il-6, il-8, il-10, tnf-α, socs3, nkap, tlr1, tlr2) in the intestine post-infection. MBC experiment demonstrated that the hepcidin synthetic peptide has an inhibitory effect on the growth of V. parahaemolyticus (32 μg/ml), A. hydrophilus (64 μg/ml), and F. columnaris (128 μg/ml), but not E. tarda (>256 μg/ml). After A. hydrophilus challenge, fpn, tf and tfr1 with peak expression at 24 hpi (2.75), 12 hpi (4.43) and 6 hpi (7.41), respectively. Hepcidin and ftn expression was highest at 48 hpi (115.01) and 72 hpi (4.16). The Fe2+ content peaked at 6 hpi (2.64 μmol/l) and reached its lowest at 12 hpi (1.12 μmol/l) in the intestine. After pathogen challenge, il-1β, il-8, socs3, tlr2, and hepcidin showed trends of increased and then decreased, with peak expression at 72 hpi (5.13, 37.05, 3.08) and 48 hpi (5.35, 115.01), respectively. These findings suggested that hepcidin plays a key role in the defense against A. hydrophila: initially restricting bacterial growth through iron metabolism (0–48 hpi), and later modulating immune responses via the TNF (by inducing il-1β and socs3) and Toll-like receptor pathways (by inducing il-8 and tlr2) (48–96 hpi). This study provides novel insights into the immune function of hepcidin in fish and its potential application in managing bacterial infections in aquaculture.