AbstractObesity is associated with the gut microbiota and has been shown to cause gut microbiota disturbances. Our previous studies have demonstrated that Miao sour soup (SS) contains abundant short‐chain fatty acids (SCFAs) which can be used as energy substrates of intestinal flora to selectively stimulate their growth and reproduction. Therefore, we explored whether the intestinal microbiota of rats with high‐fat diet‐induced obesity could be restored to normal by SS intervention. Male obese rats were divided into five groups randomly after successful modeling of obese rats: normal diet, high‐fat diet (HDF), HFD + SS, HFD with antibiotic, and HFD with antibiotic + SS. After 12 weeks of intervention, the weight and serum lipid of obese rats decreased. Furthermore, 16S rRNA analysis showed an imbalance and a decrease in the abundance and diversity of intestinal flora in obese rats, which improved after SS intervention. At the phylum level, Firmicutes increased while Proteobacteria decreased. The composition of the intestinal flora recovered at the genus level, inhibiting the reproduction of pathogenic bacteria, while the levels of SCFA‐producing bacteria such asBlautiaandLactococcusand the levels of SCFAs in cecal contents increased. In addition, SS reduced the levels of TNF‐α and IL‐6 in the intestinal mucosa of obese rats, increased the contents of PYY and GLP‐1 in colon tissue, and increased the expression of tight junction protein Occludin and ZO‐1 in the intestinal epithelium. Taken together, SS can regulate the intestinal flora of obese rats and improve the intestinal flora to facilitate weight loss and lipid reduction.