Background The bioactive compounds of ginger (Zingiber officinale), such as gingerols, diarylheptanoids, and flavonoids, are of importance to human health because of their anticancer, antioxidant, and anti-inflammatory properties. The daughter rhizomes arise from mature rhizomes, but the pungency and pharmacological quality of the two rhizome types differ substantially.Results In this study, a metabolomic analysis was performed to investigate the biosynthesis of major bioactive compounds in the mature rhizome (R) and daughter rhizome (DR) in ginger. A total of 1212 differentially accumulated metabolites with p < 0.05 and |fold change| ≥ 1 were identified, of which 399 metabolites were more highly accumulated in R samples than in DR samples, whereas 211