This study aims to investigate the effects of starch granule-associated protein (SGAP) and starch channel protein (SGCP) on the starch digestibility characteristics before and after fermentation with Lactiplantibacillus plantarum dy-1. Using selective extraction methods, we achieved efficient and targeted depletion of SGAP and SGCP with minimal structural alteration to the starch granules. Fermentation enhances the efficiency of protein removal and improves the resistance to digestion of starch. The removal of SGAP or SGCP significantly reduced RS levels and accelerated enzymatic hydrolysis, underscoring their essential role in limiting starch digestibility. Furthermore, the absence of these proteins altered the starch's physicochemical behavior, lowering gelatinization temperature and increasing viscosity, water absorption, and swelling capacity. Our results demonstrate that SGAP is vital to maintaining starch structural integrity and enzymatic resistance. These insights provide a foundation for designing starches with tailored digestibility for low-glycemic-index food applications.