The aim of this study was to investigate the changes of untreated and steamed (100 °C, 20 min), fried (150 °C, 10 min), and baked (200 °C, 30 min) sweet potato polysaccharides during in vitro digestion and their effects on the intestinal flora. The results showed that the reducing sugar content of all four sweet potato polysaccharides increased significantly during digestion. During in vitro fecal fermentation, the content of reducing sugars and total carbohydrates decreased significantly. It indicated that all four polysaccharides showed degradation of polysaccharides during fermentation. Compared to the blank group, the total SCFAs content of the four polysaccharide sample groups was significantly increased. It was worth noting that sweet potato polysaccharides increased the percentage of Bacteroidetes and decreased the percentage of Proteobacteria in the intestinal flora. The findings provide evidence that sweet potato polysaccharides regulate intestinal flora and maintain intestinal health through interactions with intestinal flora.