This study investigated the effects of dietary protein levels on disease resistance, immune function and structural integrity in the head kidney, spleen and skin of grass carp (Ctenopharyngodon idella). A total of 540 grass carp (264.11 ± 0.76 g) were fed six diets containing graded levels of protein (143.1, 176.7, 217.2, 257.5, 292.2 and 322.8 g digestible protein kg−1 diet) for 8 weeks. After the growth trial, fish were challenged with Aeromonas hydrophila for 14 days. The results indicated that optimal levels of dietary protein: (1) (1) increased the lysozyme (LA) and acid phosphatase (ACP) activities and the complement 3 (C3) and C4 contents, up-regulated antimicrobial peptides, anti-inflammatory cytokines, inhibitor of κBα, target of rapamycin and ribosomal protein S6 kinases 1 mRNA levels, whereas down-regulated pro-inflammatory cytokines, nuclear factor kappa B (NF-κB) P65, IKKβ, IKKγ, eIF4E-binding proteins (4E-BP) 1 and 4E-BP2 mRNA levels in the head kidney, spleen and skin of grass carp (P < 0.05), suggesting that optimal level of dietary protein could enhance immune function in the head kidney, spleen and skin of fish; (2) increased the activities and mRNA levels of antioxidant enzymes, enhanced the glutathione content, decreased reactive oxygen species, malondialdehyde (MDA) and protein carbonyl contents, and up-regulated the mRNA levels of NF-E2-related factor 2, B-cell lymphoma protein-2, inhibitor of apoptosis proteins, myeloid cell leukemia-1 and tight junction complexes, whereas down-regulated Kelch-like-ECH-associated protein (Keap) 1b, cysteinyl aspartic acid-protease 3, 8, 9, Fas ligand, apoptotic protease activating factor-1, Bcl-2 associated X protein and myosin light chain kinase mRNA levels in the head kidney, spleen and skin of grass carp (P < 0.05), indicating that optimal level of dietary protein could improve structural integrity in the head kidney, spleen and skin of fish. Finally, based on the skin hemorrhage and lesion morbidity, LA activity and MDA content, the optimal levels of dietary protein for grass carp (264 g-787 g) were estimated to be 241.45 g kg−1 diet (217.68 g digestible protein kg−1 diet), 301.68 g kg−1 diet (265.48 g digestible protein kg−1 diet) and 307.84 g kg−1 diet (272.71 g digestible protein kg−1 diet), respectively.