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The practice of adding probiotics in shrimp diet has increased significantly because of its beneficial effects on growth performance and disease resistance. However, little attention has been paid to marine-derived probiotics, which might be more suitable for aquatic animals. In the present study, an 8-week feeding trial was carried out to explore the effects of Shewanella sp. MR-7 in shrimp diet. Three concentrations of Shewanella sp. MR-7 (SS-MR-7, 106 colony forming units (CFU)/g diet, F1; 107 CFU/g diet, F2; 108 CFU/g diet, F3) were added to the basal diet (F0) of Pacific white shrimp. At the end of the trial, an acute ammonia stress test was performed. The results showed that supplementation with 107 CFU SS-MR-7 per g diet significantly improved shrimp weight gained and specific growth rate. A significantly higher shrimp survival rate was also observed in the F2 group after acute ammonia stress. Meanwhile, dietary SS-MR-7 induced the hepatopancreatic mRNA expression of antioxidation-related genes encoding heat shock protein 70, thioredoxin 1, and glutathione peroxidase, as well as immunity-related genes, such as those encoding lipopolysaccharide and beta-1,3-glucan-binding protein, prophenoloxidase activating factor, and prophenoloxidase. Furthermore, the intestinal microbiota was responsive to the diets. The abundance of the beneficial bacteria Pseudomonas was enriched, while the contents of potential pathogens (such as Bacteroides and Escherichia-shigella) decreased. Overall, our results indicate that SS-MR-7 could be an effective probiotic in shrimp culture as it increase growth performance, immunity and the abundance of intestinal beneficial bacterial.