To further understand the relationship between gut microbiota and liver and kidney biochemical indicators in patients with type 2 diabetes with diarrhea. We collected the flora data and liver and kidney index data of 26 patients with type 2 diabetes with diarrhea and 26 patients with type 2 diabetes. One-way variance analysis was used to analyze the differences in liver and kidney indexes between the two groups; linear regression analysis was used to analyze the relationship between liver and kidney indicators and gut microbial alpha diversity; PERMANOVA was used to analyze the difference in structure of gut microbial β diversity; then Spearman rank correlation test was used to analyze the relationship between liver and kidney biochemical indexes and gut microbiota. The results showed that there were significant differences in triglyceride (TG) and blood urea nitrogen (BUN) in liver and kidney indexes between the two groups (P=0.006, P=0.003); the increase of serum bilirubin in patients with type 2 diabetes with diarrhea was related to the decrease of the species diversity of the intestinal flora; Bacteroides, Lacetospirillum, and Prevotella in type 2 diabetes patients with diarrhea decreased, whereas Rumenaceae significantly increased. In addition, Laospirillaceae and Rumenomycetes were positively correlated with serum bilirubin, which was related to the decrease of TG and has nothing to do with the increase of BUN. There is a relationship between liver and kidney indexes of patients with type 2 diabetes with diarrhea and gut microbiota, and these bacteria can provide new targets for the treatment of type 2 diabetes with diarrhea.