According to the principle of dynamic balance of plant and animal protein nutrition, the new grain yogurt was fermented by the black sesame, black bean and corn, and free radical scavenging activities of grain yogurt were detected by the method of scavenging activities of α, α-diphenyl-β-picrylhydrazyl (DPPH) radicals and hydroxyl radicals, which commercial yogurt and unfermented grain juice were used to be compared groups. The results showed that the optimum manufacturing process of the grain yogurt was 10 mL/100 mL black sesame juice, 13.3 mL/100 mL black bean juice, 13.3 mL/100 mL corn juice, 7.9 g/100 mL milk powder, 5 g/100 mL sugar, 3 mL/100 mL inoculation density, 7 hours fermentation time, and 42 ℃ fermentation temperature. The product made by this condition was delicious and delicate texture with flavor of sweet and sour. The results of the free radical scavenging activities of grain yogurt were that the trend of increasing of the free radical scavenging activities of grain yogurt was with the increasing of the yogurt concentration. When the concentration of grain yogurt was 50 mg/mL, the scavenging rates of DPPH and hydroxyl radicals were (84.9 ± 0.10)% and (55.6 ± 0.12)%, respectively. When the yoyurt was in the same concentration, the free radical scavenging activity of grain yogurt was higher than that of commercial yogurt.