Huangjiu, the national wine of China, has the characteristics of low grain consumption, low alcohol content and high nutrition, which aligns with the world's beverage wine consumption trend. The research on glutinous rice huangjiu from southern China is more extensive, while millet huangjiu from northern China has received less attention, hindering the diversified development of huangjiu. Polysaccharides play an important role in huangjiu's health activity and flavor characteristics. In this study, the polysaccharide components in millet huangjiu were separated and identified for the first time, and the influence of polysaccharides on the flavor release was explored through sensory evaluation, SPME-GC–MS, threshold determination and isothermal titration calorimetry. The millet huangjiu polysaccharide HJ-1 was composed of →3)-α-Manp(1→, α-Manp-(1→, →2,6)-α-Manp-(1→, →3)-α-Xylp-(1→ and →3)-β-Arap-(1→. HJ-1 (0.1–1 mg/mL) could regulate the release performance of key flavor compounds in millet huangjiu, inhibit the herbal, fruity and alcoholic aromas, and promote the sweet and rice aromas. Further studies showed that HJ-1 formed complexes with ethyl acetate, acetic acid, 2,3-butanediol and γ-butyrolactone through van der Waals forces and hydrogen bonds, and the process was a spontaneous exothermic entropy reduction reaction. This study provides a new idea for optimizing the overall aroma of huangjiu and improving its sensory quality.