Shanlan red rice is a characteristic rice resource with potential for developing low glycemic index (GI) foods, and its starch physicochemical properties and digestive characteristics can be significantly affected by processing methods. To screen suitable processing methods for preparing Shanlan red rice cooked flour with a low estimated glycemic index (eGI), three treatments—baking, microwave, and high-pressure steaming—were applied to heat-treat Shanlan red rice, which was subsequently milled into flour. The eGI value, viscosity, crystalline structure, and microstructure of each sample group were determined, with raw Shanlan red rice flour as the control. The results showed that the eGI of the high-pressure steaming group (71.73±1.91) was significantly higher than that of the raw flour (61.83±1.92), baking (63.17±2.02), and microwave (65.73±1.45) groups (P<0.05); no significant differences were found among the raw flour, baking, and microwave groups. All viscosity parameters of the microwave and high-pressure steaming groups were significantly lower than those of the raw flour group (P<0.05), with a greater reduction observed in the high-pressure steaming group. Raw flour, baking, and microwave groups all exhibited A-type crystalline structure, with crystallinities of 17.85%, 13.38%, and 8.94%, respectively; the high-pressure steaming group transformed to V-type with crystallinity of 5.39%. The degree of damage to starch granules and cellular structures was consistent with the trend of eGI, and the high-pressure steaming group showed the most severe damage. The structural integrity of starch could be effectively preserved by baking and microwave treatments, while relatively low eGI values were maintained. These findings provide a theoretical basis for optimizing the processing technology of low-GI Shanlan red rice flour and for developing corresponding low-GI food products.