•Heavy-metal pollution re-shaped the composition of the GI microbiota of B. raddei..•Heavy-metal pollution reduced the proportion of probiotics in the GI microbiota of B. raddei.•Heavy-metal pollution decreased the species diversity in the GI tract of B. raddei. Gastrointestinal (GI) microbiota plays a very important role in maintaining its host’s health. However, the effects of environmental contamination on the GI microbiota homeostasis of amphibians have not yet been reported. The present study reveals the long-term effect of natural heavy-metal pollution on the GI microbial community diversity and structural changes of Bufo raddei (B. raddei). Basing on the 16S rRNA sequencing method, the GI microbiota of B. raddei from a heavily heavy-metal-polluted area (Baiyin, (BY)) and a relatively unpolluted area (Liujiaxia, (LJX)) were profiled. The results showed that heavy-metal pollution had caused significant shifts in the composition of the GI microbiota both at the phylum and genus levels. Specifically, Bacteroidetes dominated in the GI tract of B. raddei from BY, while Tenericutes was much more common in those from LJX. The ratio of Firmicutes/Bacteroidetes and the proportion of probiotics in the GI microbiota of B. raddei from BY were reduced compared to those from LJX, as well. Heavy-metal pollution also induced in a reduction of species diversity and decreased proportion of unique operational taxonomic units in the GI tract. In short, our results demonstrate that long-term heavy-metal exposure re-shaped the composition and decreased the species diversity of GI microbiota of B. raddei; our results also represent a novel approach to uncover the toxic effects of pollution on amphibians.