Deoxynivalenol (DON) is a common environmental contaminant that causes food refusal and growth retardation in animals. DON targets the intestine and is hazardous to animal, however, it is not clear whether its effect on animals is consistent. Chickens and pigs are the two main animals affected by DON exposure with different susceptibilities. In this study, we found that DON inhibited animal growth and caused damage to the intestine, liver and kidney. DON caused intestinal flora disorders in both chickens and pigs, such as changes of flora diversity and the relative abundance of dominant phyla. Functional analysis showed that changes in the intestinal flora induced by DON were mainly related to metabolic and digestive functions, indicated that the intestinal flora may be associated with the DON-induced intestinal dysfunction. Comparative analysis of differentially altered bacteria suggested that Prevotella may play an important role in maintaining intestinal health, and the presence of differentially altered bacteria in the two animals suggested that DON may have different toxicity modes in animals. In summary, we confirmed the multi-organ toxicity of DON in two major livestock and poultry animals, and speculated that the intestinal flora may be related to the toxic damage caused by DON through species comparison analysis.