Complex gels of fermented indica rice starch (FIRS) and soybean protein isolate (SPI) (0%–12%) were prepared to investigate the relationship between gel characteristics and digestive properties. During the co-gelatinization process, adding 9% SPI increased the resistant starch content from 19.83% to 30.43%, and the glycemic index decreased from 78.05 to 67.34, meaning that the glycemic index of the system changed from high to medium. Gel characteristics showed that 3% SPI enhanced the gel strength of FIRS, concurrently impeding water absorption capacity and reducing solubility. Moreover, adding SPI improved the gelatinization stability of FIRS (pasting temperature increased and breakdown decreased significantly, P < 0.05). Analysis of rheological properties revealed that hydrophobic, hydrogen bonding, and electrostatic interactions were at play between FIRS and SPI, with the hydrophobic interaction being the most prominent. Fractionation of SPI into its 11S and 7S globulin components and subsequent testing of FIRS–globulin mixtures demonstrated that 11S contributed to hydrophobic interactions and 7S contributed to hydrogen bonding, thus affecting viscoelasticity and starch order (short-range and long-range structures). Collectively, these findings suggest that SPI hinders the digestion of FIRS through hydrophobic interactions and the inhibition of gelatinization.