This study aimed to investigate the effects of choline deficiency on intestinal inflammation of fish after Aeromonas hydrophila infection and the potential molecular mechanisms. Juvenile Jian carp (Cyprinus carpio var. Jian) were fed two diets containing choline at 165 (deficient group) and 607 mg/kg diet respectively for 65 days. Choline deficiency decreased intestinal lysozyme activity, C3 and IgM contents, increased acid phosphatase activity, downregulated mRNA levels of antimicrobial peptides [liver-expressed antimicrobial peptide (LEAP) 2A, LEAP-2B, hepcidin and defensin], cytokines [interleukin (IL) 6a, tumor necrosis factor α (TNF-α), interferon γ2b (IFN-γ2b), IL-6b and transforming growth factor β2 (TGF-β2) only in proximal intestine, IL-10 in mid and distal intestine], immune-related signaling molecules [Toll-like receptor 4 (TLR4), myeloid differentiation primary response 88 (MyD88), nuclear factor kappa B (NF-κB), inhibitor of NF-κB (IκB), Janus kinase 3 (JAK3), and signal transducers and activators of transcription 5 (STAT5)], tight junction proteins (claudin 3b, claudin 3c, claudin 11 and occludin), and mitogen-activated protein kinases p38 (p38MAPK) in proximal and distal intestine of juvenile Jian carp after A. hydrophila challenge. In contrast, choline deficiency upregulated mRNA levels of antimicrobial peptides (LEAP-2A, LEAP-2B, hepcidin and defensin), cytokines (IL-6b, IFN-γ2b and TGF-β2), immune-related signaling molecules (TLR4, MyD88, NF-κB, IκB, JAK3, STAT4 in three intestinal segments, and STAT6), claudin 11, and p38MAPK in mid intestine of fish. This study provides new finding that choline deficiency-induced immune responses against A. hydrophila infection were varied among three intestinal segments in fish.