The aim of this study was to explore the anti-obesity activity of thinned peach polyphenols (TPP) and their effects on gut microbiota. An obese mouse model was established using a high-fat diet, and high-throughput sequencing was used to analyze changes in gut microbiota in mice fed with TPP. The results showed that dietary TPP reduced body weight, promoted appetite, reduced liver injury, and reduced levels of TC, TG, LDL-C, ASL and ALT while increasing HDL-C. TPP also enhanced the richness and diversity of gut microbiota in later stages of feeding. Composition and correlation analysis indicated that TPP increased probiotics (such as Alistipes, Akkermansia, Klebsiella, Bacteroides) which negatively correlate with obesity. TPP also reduced the numbers of harmful bacteria (including Helicobacter, Anaeroplasma), which positively correlate with obesity. Probiotics and harmful bacteria cluster independently and the two groups affect each other negatively. These results suggest that TPP reduced obesity by affecting the composition of the gut microbiota in mice. TPP can therefore be used as an ingredient in food to prevent the development of obesity.