The present study preliminarily investigated the effects of high level of fermented soybean meal (FSBM) protein substituted for fish meal (FM) protein on the growth and intestinal homeostasis of pearl gentian grouper. Seven hundred and twenty juvenile groupers were randomly divided into three groups, including the FM control group, 20% FSBM protein substituted for FM protein group (FSBM20) and FSBM40 group (n = 4). Three iso-nitrogenous and iso-lipidic diets were prepared and fed to fish for 10 weeks. Each barrel of cultural water is 1 m3, using natural light and temperature. Results showed that weight gain, specific growth rate, intestine plica length/width and microvilli length in FSBM groups decreased significantly (p < .05), and the lamina propria width in FSBM groups increased significantly (p < .05). The enzyme activities of glutathione reductase, glutathione peroxidase and total superoxide dismutase in distal intestinal tissues and alanine aminotransferase and aspartate transaminase in liver tissues increased significantly with dietary FSBM addition (p < .05). The pro-inflammatory and immune-related gene expressions of IL1β, IL12, IL32 and TNF-α increased significantly in FSBM40 group (p < .05), while the anti-inflammatory and immune-related gene expressions of IL5, IL10, IgM, CD4 and lysozyme decreased significantly in FSBM40 group (p < .05). The aquaporin protein gene expressions of aqu1, aqu4 and aqu12, and the tight junction protein gene expressions of jam, claudin3, claudin12, claudin15 and ZO-3 decreased significantly (p < .05), while the gene expressions of aqu8, aqu9, aqu10 and ZO-1 increased significantly (p < .05), and the ion transport carrier gene expressions of nkcc and clc decreased significantly (p < .05). 16S high-throughput sequencing showed that at the phylum level, the abundance of Proteobacteria decreased significantly in FSBM40 group (p < .05), while that of Bacteroidetes, Firmicutes, Acidobacteria and Actinobacteria increased significantly in FSBM40 group (p < .05). At the genus level, the top 10 species were Photobacterium, Stenotrophlomonas, Vibrio, Phyllobacterium, Chromohalobacter, etc. The abundance of Photobacterium in FSBM40 group decreased significantly (p < .05), while that of other species increased significantly (p < .05). High level of FSBM substituted for FM resulted in a significant decrease in the functional abundance of aerobic_chemoheterotrophy and chemoheterotrophy in FSBM40 group (p < .05), while animal_parasites_or_symbiont abundance increased significantly in FSBM40 group (p < .05). Present study showed that experimental level of FSBM had a significantly negative effect on the growth performance, intestinal mucosa structure and intestinal flora composition in pearl gentian grouper.