Abstract: To investigate the ameliorative effects of Bacillus licheniformis FA6 on intestinal health impairment induced by a high soybean meal diet of grass carp (Ctenopharyngodon idella), four isonitrogenous and isolipidic diets were formulated as follows: a basal diet with 18% fish meal and 10% soybean meal (positive-control group, PC), a high soybean meal replacement diet with 2% fish meal and 35% soybean meal (negative-control group, NC), and the NC diet supplemented with 10⁶ CFU/g (low-dose group, LD) or 10⁸ CFU/g (high-dose group, HD) of B. licheniformis FA6. Subsequently, Enzyme-linked immunosorbent assay, hematoxylin and eosin tissue staining, Real-time fluorescence quantitative PCR, and Illumina MiSeq high-throughput sequencing were employed to assess intestinal barrier function, immune capacity, gene expression, and microbiota structure. The results showed that compared to the PC group, the villus height and muscular thickness in the foregut and midgut of the NC group were significantly reduced (P<0.05); serum levels of Immunoglobulin M (IgM), complement 3 (C3), and interleukin-22 (IL-22) were significantly decreased, while D-Lactic Acid (D-LA) content was markedly increased (P<0.05). After adding B. licheniformis FA6 to the high soybean-meal diet, compared to the NC group, the HD group exhibited significantly increased villus height in the foregut, midgut, and hindgut, as well as increased muscular thickness in the foregut (P<0.05); serum levels of C3, IgM, lysozyme, and IL-22 were significantly elevated, while D-LA content was significantly reduced (P<0.05). Intestinal immune-related gene HYOU1 expression was down-regulated and IRF10 expression up-regulated (P<0.05). The relative abundances of Bacillus and Cetobacterium were significantly increased (P<0.05), whereas those of Desulfovibrio, Enterobacter, Clostridium, and Flavobacterium were significantly decreased (P<0.05). In conclusion, high replacement of fish meal with soybean meal impairs intestinal barrier function, reduces immunity, and induces enteritis in grass carp. Supplementation with 10⁸ CFU/g B. licheniformis FA6significantly improves intestinal barrier function and enhances immunity, thereby alleviating soybean-meal-induced enteritis.