With increasing fish density in aquaculture systems, residual bait and a large amount of metabolic waste from over-feeding are accumulated in the water. These are then converted into ammonia nitrogen through ammonization. This, in turn enriches the water body, and does harm to the nervous, respiratory, and antioxidant systems of fish. The present study was conducted on Qi river crucian carp () larvae[body weight (15±2) g] to investigate the histological damage of excessive ammonia nitrogen (50 mg/L, 100 mg/L, 150 mg/L, 200 mg/L, 250 mg/L, and 300 mg/L) on brain, gill, liver, and kidney tissues. The results showed that the highest safe ammonia nitrogen concentration was 16.6 mg/L. Once the concentration of ammonia nitrogen was higher than the safe concentration, the structure of nerve fibers in brain tissue was destroyed, and the secretory and Sertoli cells showed different degrees of necrosis; the gill lamella showed different degrees of atrophy and aggregation, the base of gill filaments was congested and swollen, and the space between gill filaments was enlarged. Ultramicroscopic observation revealed that the sputum smear appeared atrophied, epithelial cells fell off, and secretion on the cell surface increased. As for the liver, the arrangement of hepatocytes around the central vein of liver tissue presented different degrees of disorder, the contours of hepatic lobules were blurred, and the nuclei showed different degrees of migration and dissolution. Ultramicroscopic observation showed that after 96 h of ammonia nitrogen stress, the distance between the hepatic lobules increased, the arrangement between hepatocytes was lost, the surface of cells was rough, and secretions increased. In the kidney, renal cysts were enlarged, lymphocytes exhibited infiltration and spreading, renal tubular lumen shrinkage was more serious, and glomerular necrosis occurred. The above results indicate that high concentrations of ammonia nitrogen cause different degrees of damage to the nerves, respiratory, and metabolic-related organs of Qi River crucian carp. Thus, the toxicity of ammonia nitrogen in high-density culture cannot be ignored. Therefore, we should strictly monitor the concentration of ammonia nitrogen in the culture water body and practice green and healthy cultivation.