Cadmium (Cd) is known to be a potentially toxic heavy metals to the fish health and growth. Carassius auratus gibelio (C. a. gibelio) specimens were exposed to waterborne Cd (0, 0.05, 0.10, 0.15, and 0.20 mg/L CdCl2) for 14 days. Cd accumulation, liver and intestine histopathology, and intestinal microorganism were investigated in the present study. The results indicated that Cd accumulation in the gill, liver, intestine, and muscle gradually decreased as Cd concentration increased. The gill accumulated higher amounts of Cd than other tissues. The histopathology of liver and intestine underwent changes with different Cd concentrations, including hepatocyte hypertrophy, aggregation of blood cells, sinusoids, lipidosis, necrosis of hepatic tissues, the erosion of villi, necrosis in the mucosal layer, the appearance of vacuoles in the lamina propria, hyperplasia, and swelling of goblet cells. Moreover, the core gut microbiota existed in the intestinal microorganism and did not change as Cd concentration increased. However, the diversity of intestinal microorganism was significantly reduced compared with that of the control sample. The present results indicated that C. a. gibelio exposed to Cd suffered toxicity, and Cd could affect the biodiversity of the intestinal microbiota of C. a. gibelio.