Polygonatum cyrtonema Hua (PCH) belongs to the genus Polygonatum Mill of the Liliaceae family. As a traditional tonic herb, the rhizome of PCH has been widely used as a functional food and traditional Chinese medicine, mainly for the treatment of spleen and lung Qi deficiency, essence and blood deficiency, internal heat, and thirst. To further elucidate the unknown chemical composition of PCH, this study presents an analytical strategy using macroporous resin (D101) column chromatography combined with ultra-high-performance liquid chromatography-Q-Exactive Orbitrap mass spectrometry (UHPLC-Q-Exactive Orbitrap MS) for the characterization of PCH’s chemical composition. The PCH extracts were separated via D101 resin column chromatography in conjunction with reverse phase liquid chromatography (C18 column). They were then analyzed by Q-Exactive Orbitrap mass spectrometry utilizing parallel reaction monitoring (PRM) mode, diagnostic fragment ions (DFIs), and neutral loss (NL). A total of 153 compounds were identified through comparing the mass spectrometry data with standard references, the published literature, and public databases, including 40 alkaloids, 43 organic acids, 30 flavonoids, 17 saponins, and 23 other compounds; The result expands PCH’s chemical composition, enhancing our understanding of its therapeutic effects and quality assurance. At the same time, the strategy has the potential to show a wide range of applications in the chemical characterization of different samples.