This study investigated the impact of dietary fiber from sweet potato residue (SPDF) on the diversity of the gut microbiota. An in vitro batch culture system simulating the human gut was used to understand the prebiotic role of SPDF. The results showed that SPDF mediated a significant increase in the concentrations of Bifidobacterium and Lactobacillus, whereas induced a significant decrease of Enterobacillus, Clostridium perfringens and Bacteroides. The prebiotic index and Bifidobacterium/Enterobacillus value were also significantly increased in SPDF groups compared to those of the control group, suggesting that SPDF had prebiotic effects. Furthermore, to investigate the effects of SPDF on the intestinal microecosystem, diets containing different concentrations of SPDF were used to feed Wistar rats for 4 weeks. 16S rRNA gene sequencing, short chain fatty acid quantification and physiochemical property analysis in the rat feces were then conducted. The results showed that SPDF significantly increased the Bacteroidetes to Firmicutes ratio at the phylum level and the amount of Akkermansia was also increased at the genus level, which was confirmed by qRT-PCR. The production of propionate and butyrate in the rat feces of both 3% and 15% SPDF groups was higher than that in the control group, which was further confirmed by the decrease of pH. Additionally, SPDF supplementation in this study resulted in a higher villus height to fossa depth ratio, which indicated improved digestion and absorption in the GI tract. Our findings support the utilization of SPDF from sweet potato residue in the development of potentially prebiotic food products for improving intestinal health.