A 12-week feeding trial was conducted to investigate the effects of dietary soyasaponins on the growth performance, activities of digestive enzymes, intestinal morphology and intestinal bacterial community of turbot (Scophthalmus maximus). Two isonitrogenous and isolipidic experimental diets (based on 67% fish meal) containing 0% and 0.3% soyasaponins were formulated. The results showed that the growth performance was not affected by dietary soyasaponins, while the activities of intestinal pepsin and amylase were significantly depressed by dietary 0.3% soyasopnins. No obvious changes of intestinal histology were observed between two groups. However the gene expression of intestinal tight junction protein occludin was significantly declined when 0.3% soyasaponins was added. The analysis of intestinal microbiota showed that Proteobacteria and Halomonas were the most dominant phylum and genus in S. maximus intestine, respectively. LEfSe and MetaStat analysis showed that the abundance of dominant bacteria (Proteobacteria and Shewanella) was significantly increased by dietary 0.3% soyasaponins. Meanwhile, dietary soyasaponins significantly increased the abundance of intestinal saponin-hydrolyzing bacteria. In addition, the abundance of some intestinal potential pathogenic bacteria such as Methylobacterium, Moraxella and Photobacterium, was increased while that of some other pathogenic bacteria such as Ralstonia was decreased by dietary soyasaponins. In conclusion, dietary 0.3% soyasaponins depressed the activities of digestive enzymes, and the gene expression of intestinal tight junction protein Occludin, and altered the intestinal microbiota of S. maximus. Thus, the effects of soyasaponins on fish intestine health, especially intestinal flora, cannot be ignored and deserve funther study.