Fagao is one of China’s traditional gluten-free staple foods made with rice or corn flour. Corn Fagao prepared by co-fermentation with sourdough and yeast exhibits better quality and less staling compared to traditional yeast-fermented Fagao. The physicochemical properties of corn Fagao batter during sourdough–yeast co-fermentation were investigated. The results showed that compared with yeast fermentation, the gas production and viscosity of the batter increased with co-fermentation. The co-fermented batter showed a higher hydrolysis of starch and less amylose content. The integrity of starch granules in the co-fermented batter was damaged more seriously, and the crystallinity and short-range ordered structure were less than in the yeast-fermented batter, even though the crystal structure type of starch did not obviously change. The peak viscosity, minimum viscosity, final viscosity, decay value, and recovery value of the corn batter were reduced by co-fermentation, which improved the thermal stability of the batter and slowed down the aging. Co-fermentation also resulted in a more pronounced reduction in protein subunit content than yeast fermentation. The changes in the physicochemical properties of the corn Fagao batter help explain the improvement in quality of corn Fagao made from the co-fermentation method and may provide theoretical references for co-fermentation with sourdough and yeast to other gluten-free foods.