The relationship between the tissue structure of rice grains prepared using stepwise degrees of polishing (DOP) and starch digestibility was investigated in this study. Brown rice grains (Oryza sativa L. cv. Koshihikari) was precisely polished to 1, 3, 5, 7, and 10% (w/w) of the original weight using a pressure-type rice polisher and then cooked using a standardized cooking procedure. Although the total starch content of cooked grains had a significant tendency to increase with an increase in the DOP (77.64–84.16% db), the resistant starch content was constant between the cooked grains with different DOP (0.32–0.43% db). Cooked brown rice grains had significantly lower starch hydrolysis (65.68 vs. 89.74–96.17%) and estimated glycemic index (72.50 vs. 84.95–92.90) than polished grains after in vitro gastro-small intestinal digestion. The results revealed that starch digestibility of cooked brown rice grains was not proportional to DOP. The bran layer remained intact and covered a smaller area of the endosperm as DOP increased. In conclusion, the starch digestibility of cooked stepwise polished rice grains was affected by the bran layer on the outermost surface, which was equivalent to 1% of the weight of the brown rice grains. However, it was not affected by the ratio of the bran layer remaining on the cooked grain surface. The results of this study could contribute to the development of new agricultural machinery products that solve problems related to the control of GI of rice and rice products.