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The fish pathogen Aeromonas hydrophila causes gastrointestinal tract infections and hemorrhagic septicemia and represents a widespread risk in aquaculture. This study aimed to determine whether compound probiotics could improve the intestinal barrier, immunity, and meat quality of common carp infected by A. hydrophila by feeding them compound probiotics. Carp were assigned to one of four groups: (1) control (no infection, no probiotics); (2) control + probiotic; (3) A. hydrophila infected; and (4) the A. hydrophila + probiotic group. At the beginning of the experiment, the carp were injected with either saline (0.86%) or A. hydrophila (4.87 × 107 CFU/mL). After 2 weeks of the feeding regime, results suggested that in A. hydrophila infected carp, dietary probiotics regulated the intestinal microflora as evidenced by a reduced abundance of Proteobacteria and increased amounts of Firmicutes and Fusobacteria in the intestine. In addition, dietary probiotics ameliorated both villus swelling and the decrease in villus height induced by A. hydrophila (P