The gut microbiome plays a pivotal role in human health and is affected by various factors. To investigate the association between phenotypic and microbiota-related changes in the gut and a raw starch-based diet, we fed mice with different starch substitutes (corn, wheat, rice, and potato) for 16 weeks. The potato starch-fed group showed the lowest weight gain and fat tissue accumulation of all the groups, as well as the highest insulin sensitivity. Taxonomic analysis indicated that the proportions of Akkermansia, Rikenellaceae, and Sutterella showed the greatest increase in the ceca of mice fed raw potato starch. In addition, the gut microbiota of the raw potato starch group showed the highest carbohydrate and energy metabolism of all the groups, as confirmed by cecal metabolite analysis. The raw potato starch group also produced the highest propionic acid content. Our results showed that the differences in the digestibility of each starch, differences in the phenotype in terms of digestibility, and changes in intestinal microbiota were connected, and it was confirmed that potato starch, which had the lowest digestibility, caused the greatest difference in intestinal microbe composition and metabolism.