Based on the amino acid score (AAS), chemical score (CS), and amino acid proportional coefficient score (SRCAA) as evaluation indicators, millet powder, whey protein isolate powder, and soybean protein isolate powder were mixed to make millet compound powder. After the millet compound powder and water were uniformly mixed at a material-to-liquid ratio of 1:20, the kefir fermented millet nutritional milk was prepared by beating, gelatinizing, liquefying, saccharifying, and fermenting. The protein content, polyphenol content, viable count and acidity of kefir millet fermented milk were significantly higher than those of the other two commercially available similar beverages. The scavenging rates of DPPH free radicals and hydroxyl radicals in the kefir millet fermented milk group at three stages (before undigested, after gastric digestion for 2.5 h, and after intestinal digestion for 2.5 h) were significantly higher than those in the unfermented millet pulp group. Novelty impact statement In this study, based on the amino acid pattern and amino acid nutrition evaluation methods (AAS, CS, SRCAA), millet flour and two protein powders with rich lysine content (whey protein isolate powder and soybean protein isolate powder) were rationally compounded as amino acid balanced millet compound powder. The millet compound powder is fermented by Lactobacillus kefir into millet nutritional fermented milk with unique flavor of probiotic fermentation. The antioxidant activity of millet nutritional fermented milk and millet pulp before fermentation was compared and analyzed by gastrointestinal digestion simulation in vitro, and it was determined that millet nutritional fermented milk had strong antioxidant activity.