Microcystin-LR (MC-LR), produced by Cyanobacteria, is being detected in many types of waters, posing a universal threat to aquatic animals. However, there have been few comprehensive endpoints assessed, including oxidative stress, transcriptome changes, intestinal microbiota, and histopathology, in anurans exposed to MC-LR. In this study, all these effects of MC-LR on Chinese brown frog (Rana chensinensis David, 1875) tadpoles were investigated by exposing the tadpoles to MC-LR at different concentrations (0, 0.1, 1.0, 5.0, and 10.0 μg/L) for 7 days. Our results revealed that treatment of tadpoles with the high MC-LR dosage (10.0 μg/L) induced a significant increase in malondialdehyde (MDA) content and decreases in superoxide dismutase (SOD) activity, glutathione peroxidase (GPx) activity, and total antioxidant capacity (TAC). RNA-seq analysis of the liver showed that the number of differentially expressed genes (DEGs) was 2361 under lower MC-LR stress (1.0 μg/L), while the number of DEGs increased to 3185 under higher MC-LR stress (10.0 μg/L). Gene Ontology analysis showed that several biological processes and molecular functions related to digestion were enriched in both MC-LR treated groups, such as digestion, serine-type endopeptidase activity, and serine-type peptidase activity. KEGG enrichment analysis also indicated that the digestion for pancreatic secretion, protein digestion and absorption, and fat digestion and absorption pathways were significantly enriched in the treatment groups. Additionally, the bacterial richness was elevated by MC-LR exposure. At the phylum level, treatment with MC-LR changed the relative abundances of Desulfobacterota, Fusobacteriota, and Actinobacteriota. At the genus level, MC-LR caused significant alterations in the abundances of 23 genera. Furthermore, examination of sections obtained from the livers and intestines of tadpoles in the treatment groups showed damaged histological structure. The knowledge from this study will have potential value for understanding the mechanisms related to MC-LR toxicity in anurans.