The aquaculture industry has a shortage of objected protection against soybean meal-induced enteritis (SBMIE) in carnivorous fish caused by soybean meal feed. Our initial study discovered that Lithospermum erythrorhizon (LE) ethanol extract has potential application value in improving SBMIE. A feeding trial (for eight weeks) was conducted to investigate LE ethanol extract on pearl gentian grouper SBMIE of protection to clarify the influence of LE ethanol extract on the immune tolerance profile. Three hundred and sixty pearl gentian groupers were administered one of three distinct dietary regimes: 1) 100 % fish meal (FM); 2) soybean meal substitution of 50 % fish meal protein (SBM); 3) SBM diet +0.2 % LE ethanol extract (SBMLE). Each treatment included three 1000 L cisterns-each of cisterns with 30 fish. The preliminary weight of the fish varied between 72.01 g and 72.50 g. Growth performance results showed that WGR and SGR were significantly decreased in the SBM group (P < 0.05), while there was no significant difference between the FM and SBMLE groups. There was no significant difference in survival among the three groups. The results showed that SBM-fed fish exhibited enteritis manifested by mucosal fold shortening, lamina propria widening, decreased serum immune markers (IgM, C3, and C4), and up-regulated expression of pro-inflammatory cytokines (il17 and il12) and immune-related gene (tlr3, and tlr9). The addition of 0.2 % LE ethanol extract to the SBM diet, reversed the above symptoms, and anti-inflammatory cytokine (tgf-β1), gene expression increased significantly (P < 0.05). Intestinal transcriptome analysis exhibited that the DEGs between the FM group and the SBM group were mainly enriched in FoxO signaling pathway, while the DEGs between the SBM group and the SBMLE group were enriched in MAPK signaling pathway and FoxO signaling pathway. The RT-qPCR results also revealed changes in MAPK/FoxO signaling pathway-related genes, including Dusp1, jund, Irs2b, fbxo32, and ccng2. Overall, Lithospermum erythrorhizon ethanol extract may alleviate SBMIE by regulating MAPK/FoxO signaling pathway, which would be beneficial for enhancing the immune tolerance and utilization efficiency of pearl gentian groupers to dietary soybean meal.