This study aims to understand the functional component compositions of traditional herbal health beverages made from Polygonatum cyrtonema rhizomes and to reveal the pharmacodynamic chemical basis for their claimed health benefits. Two traditional methods, rhizome decoction and rhizome infusion, were used to make health herbal beverages, including Huangjin tea and Huangjin wine, respectively. The secondary metabolites of Huangjin beverages were investigated and compared by widely targeted metabolomics. The results clearly showed that the major functional components in Huangjin beverages were phenolic acids, flavonoids, and alkaloids. The Huangjin wine has a greater variety of flavonoids and alkaloids than Huangjin tea, and the functional components in Huangjin wine were more abundant than those in Huangjin tea. Homoisoflavones and amide alkaloids were the dominating flavonoids and alkaloids in Huangjin wine, respectively. Continuous rhizome infusion could not increase the content of functional components in Huangjin wine. In conclusion, this study not only provides primary evidence to support the claimed health benefits of Huangjin beverages but also suggests that making traditional herbal beverages by rhizome infusion has superior health benefits than making them by rhizome decoction, which is attributed to the higher yields of functional components extracted by Chinese liquor than hot water. Therefore, Chinese liquor shows advantages in its use as a superior binary ethanol-water solvent in making herbal health beverages to enhance the solubility of poorly water-soluble functional components.