AbstractDioscorea polystachya, named Chinese yam, is widely cultivated as a functional food and natural medicine in China. There is currently little information about the chemical characteristics ofDioscorea polystachyain different organs (tuber cortex and tuber flesh) and at various ages. In this study, an ultra‐high‐performance liquid chromatography coupled to quadrupole time‐of‐flight mass spectrometry (UPLC‐QTOF/MS) was used to profile chemical compounds inDioscorea polystachya. As a result, thirty‐eight compounds were detected in yam tuber cortex and tuber flesh. More compounds were detected in yam tuber cortex than in tuber flesh. Compounds such as dehydroepiandrosterone, allantoin and flavonoids were selected as biomarker candidates. Dehydroepiandrosterone was found more abundant in tuber flesh, while allantoin and flavonoids showed higher levels in tuber cortex. Furthermore, the levels of dioscin, malvalic acid and sucrose differed significantly among age groups and were highest in the tubers at 2 years. While the levels of allantoin, adenosine and glutamine increased with the growing years and were highest at 4 years. Thus, 2‐year oldDioscorea polystachyatubers could be harvested to prepare dioscin, malvalic acid and sucrose supplements. The 4‐year‐oldDioscorea polystachyatubers would be the best choice for obtaining a large amount of allantoin and adenosine in industrial production.