Abstract: Ammonia-N is one of the main pollutants in intensive culture environment and can cause serious oxidative stress and immune damage to aquatic organisms. Liver and intestinal are important defense mechanisms to protect organisms from biotic and abiotic stresses, however, the response mechanism of liver and intestine to ammonia stress in Macropterus salmoides remains unclear. We investigated the response mechanism of liver and gut to ammonia nitrogen stress in juvenile Macropterus salmoides, three concentrations of 0, 25 and 50 mg/L (Non-ionic ammonia concentrations of 0, 0.55 and 1.11 mg/L) were set for larval Macropterus salmoides (15.32±0.65) g in order to study the effects of ammonia-N stress for 48h on liver and intestinal tissue structure, enzyme activities and intestinal microorganisms of Macropterus salmoides. The results showed that after 48h of ammonia stress, both 25 and 50 mg/L ammonia-N stress caused hepatocyte vacuolization and hepatocyte arrangement disorder in liver tissue. In addition, 50 mg/L ammonia-N stress increased the number of goblet cells in intestinal tract, villus width and muscle layer thickness. The activities of GPT and GOT in liver tissue of 25 and 50 mg/L groups were significantly decreased compared with the control group. The LZM activity in liver tissue, SOD activity, CAT activity and MDA content in intestinal tissue were significantly higher than those in the control group (P<0.05). The activity of complement C3 in 50 mg/L group was observably higher than that in the control group (P<0.05). Ammonium-nitrogen stress affected Alpha and Beta diversity significantly. At the phylum level, the relative abundance of Bacteroidetes and spirochetes in 50 mg/L group was significantly increased compared with the control group (P<0.05). At the genus level, the abundance of Acinetobacter, Chryseobacterium and Brevinema in the 50 mg/L group was remarkably higher than that in the control group, while the abundance of Plesiomonas was significantly decreased (P<0.05). The results of BugBase phenotype prediction showed that Gram-negative bacteria were absolutely dominant in the intestinal flora. Moreover, intestinal flora in 50 mg/L group had lower biofilm formation ability and stress tolerance. This study showed that ammonia nitrogen stress caused damage to the liver and intestinal tissues of Macropterus salmoides, and decreased the metabolism and detoxification ability of the fish. The activity of antioxidant enzymes increased, and the Macropterus salmoides developed oxidative stress. The activities of lysozyme and complement C3 rised, GOP and GPT activities decreased, and the ability of non-specific immune system decreased at the same time, the composition of intestinal flora is changed, the stress tolerance of intestinal flora is reduced, and the intestinal function is easily damaged. This study will provide a theoretical basis for analyzing the harm of ammonia-N to fish.