A 12-week feeding trial was conducted to investigate the potential protective effects of citric acid against soybean meal-induced intestinal oxidative damage and micro-ecological imbalance in juvenile turbot (S. maximus L.). Four isonitrogenous and isolipidic experimental diets, that is fish meal-based diet (FM), FM with 40% fish meal protein replaced with soybean meal protein diet (SBM), supplemented with 1.5% citric acid (1.5% CA) or 3% citric acid (3% CA). Results showed that both citric acid diets significantly enhanced the total antioxidative capacity and the gene expression of superoxide dismutase, glutathione peroxidase and heme oxygenase 1, while also decreasing the malondialdehyde content in the distal intestine. Compared to diet SBM, the genes expression of p53, protein kinase C and Caspase-3 were remarkably declined by dietary citric acid supplementation, while the genes expression of proliferating cell nuclear antigen and mucins showed an opposite trend. The structural integrity of the distal intestine in fish fed citric acid was showed in the histological results. Sequencing of bacterial 16s rRNA V4 region showed that the profile of intestinal bacteria was altered by dietary citric acid supplementation, which was supported by the diet-cluster of PCoA and phylogenetic tree. MetaStat analysis indicated that dietary citric acid dramatically reduced the relative abundance of the Vibrio genus. In conclusion, dietary citric acid mitigated soybean meal-induced intestinal oxidative damage, beneficially alleviated the micro-ecological imbalance and specifically reduced the relative abundance of the Vibrio genus in the distal intestine of juvenile turbot.