Bacterial disease infections pose a major challenge to the healthy growth of crucian carp. Hawthorn polysaccharide (HP) is a natural active ingredient in hawthorn and has a wide range of pharmacological effects. However, the mechanism of HP against Aeromonas hydrophila infection in crucian carp cultures is unknown. In this study, it was found that 0.4% HP could significantly reduce the mortality of crucian carp, significantly increase the activities of T-AOC, SOD, CAT, and GSH-PX of crucian carp infected with A. hydrophila (p < 0.05), decrease the activity of MDA, and decrease the expression levels of TGF-β, TNF-α, IFN-γ, and IL-8 genes. Increased IL-10 gene expression levels (p < 0.05) significantly improved the disease resistance of crucian carp. HP could relieve intestinal inflammation caused by A. hydrophila infection, restoring intestinal structural integrity. At the same time, HP increased the diversity and improved the structure of intestinal microbiota. At the phylum level, the abundance of Proteobacteria and Firmicutes increased, while that of Bacteroidota and Fusobacteriota decreased. At the genus level, the abundance of Aeromonas increased, while the abundance of Cetobacterium decreased. Non-targeted metabolomics analysis of crucian carp LC-MS revealed 147 different metabolites, 62 of which were up-regulated and 85 of which were down-regulated, and Linoleic acid metabolism and Glycerophospholipids were one of the most important metabolic pathways. In conclusion, the supplementation of HP in feed can promote the healthy breeding of crucian carp, and the effect of resisting A. hydrophila is better.