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Beany flavor is a traditional sensory indicator for evaluating the quality of Radix Astragali (RA or "Huangqi" in Chinese). A RA root with a strong beany flavor is considered to be good quality in Chinese medicine. However, there is neither a study reporting volatile compounds contributing to RA beany flavor nor the relevance between beany flavor and the quality of RA. In this study, we assessed the quantification of beany flavor substance and main bioactive metabolites. The results showed that hexanal was a major volatile component contributing to the beany flavor in RA. The value of hexanal was significantly related to the origin and growth age of RA, indicating that the component could be used as a volatile indicator for the distinction of RA. Statistical analysis further demonstrated that hexanal, astragaloside IV, and total polysaccharides were primary indicators and total isoflavonoids, astragalosides, calycosin, and formononetin were the secondary indicators for quality control of RA. Correlation analysis showed that the level of hexanal was positively associated with the concentration of astragaloside IV and total polysaccharides. Our study demonstrated that aroma is one of the most important quality attributes of RA and will help to understand the role of aroma in quality assessment of traditional Chinese medicines.