The age of the ginseng plant has been considered as an important criterion to determine the quality of this species. For age differentiation and structure interpretation of age-dependent key constituents of Panax ginseng, hairy root (fine root) extracts aged from four to six years were analyzed using a nontargeted approach with ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS). Various classification methods were used to determine an optimal method to best describe ginseng age by selecting influential metabolites of different ages. Through the metabolite selection process, several age-dependent key constituents having the potential to be biomarkers were determined, and their structures were identified according to tandem mass spectrometry and accurate mass spectrometry by comparing them with an in-house ginsenoside library and with literature data. This proposed method applied to the hairy roots of P. ginseng showed an improved efficiency of age differentiation when compared to previous results on the main roots and increases the possibility of the identification of key metabolites that can be used as biomarker candidates for quality assurance in ginseng.