In order to explore the effects of chestnut skin and inner skin bound polyphenols on the intestinal microbiota of SD rats, an in vitro colonic fermentation model was constructed, which was divided into chestnut skin bound polyphenols (CSBP) group, chestnut inner skin bound polyphenols (CISBP) group and control (CK) group, and the microbial diversity analysis of the three groups was determined by 16S rRNA high-throughput sequencing technology. The results showed that compared with the CK group, the relative abundance of intestinal microbiota in the CSBP group and CISBP group increased overall, the ratio of Bacteroidetes to Firmicutes increased, and the relative abundance of beneficial bacteria such as Lactobacillus and Intestinimonas significantly increased. However, the relative abundance of harmful bacteria such as Dorea and Clostridiales significantly decreased. In addition, the function prediction showed that CSBP had the effects of promoting cell growth and reconstruction, maintaining the normal function of tissues and organs, scavenging free radicals and toxic substances, and reducing cell damage and inflammation. CISBP could promote fat metabolism, blood sugar regulation, neurotransmitter synthesis, and protein construction. It could be concluded that CSBP and CISBP had an effect on the intestinal microbiota, promoting beneficial bacteria and inhibiting harmful bacteria by increasing the abundance of intestinal microbiota, and the intestinal microbiota of SD rats developed towards a healthier composition. This study aimed to provide a reference for further development of chestnut resources and the research and development of functional foods that could regulate intestinal microbiota.