The intestine is the main organ for nutrient absorption in amphibians. It is sensitive to atrazine, which is a herbicide widely used in agricultural areas. At present, there is a lack of systematic research on the effect of atrazine on the amphibian intestine. In this study, we evaluated the effects of atrazine exposure (0, 50 μg/L, 100 μg/L, and 500 μg/L) for 20 days on intestinal histology, microbiota and short chain fatty acids in Pelophylax nigromaculatus tadpoles. Our research showed that 500 μg/L atrazine exposure significantly decreased the height of microvilli and epithelial cells, and altered the composition and diversity of intestinal microbiota in P. nigromaculatus tadpoles compared to the control. At the phylum level, the abundance of Bacteroidetes and Fusobacteria increased significantly, while that of Verrucomicrobia and Firmicutes decreased significantly in the 500 μg/L atrazine treatment group. At the genus level, Akkermansia and Lactococcus had significantly lower abundance in the 100 μg/L and 500 μg/L atrazine exposure group, while Cetobacterium was only detected in the 100 μg/L and 500 μg/L atrazine treated group. Also, function prediction of intestinal microbiota showed that atrazine treatment significantly changed the metabolism pathways of P. nigromaculatus tadpoles. In addition, 500 μg/L atrazine exposure changed the content of short chain fatty acids by significantly increasing the content of total SFCAs, butyric acid, and valeric acid, and decreasing the content of isovaleric acid in the intestine. Taken together, atrazine exposure could affect the intestinal histology and induce intestinal microbiota imbalance and metabolic disorder in amphibian tadpoles.