In the current study, liquid chromatography-mass spectrometry combined with multivariate statistical analyses was employed to investigate the time-varying biochemical changes during the pile-fermentation process with the emphasis on the active ingredients to clarify the manufacturing process of ripened pu-erh tea as a whole. The metabolite profiles of different manufacturing processes were unique and could be distinguished with the aid of principal component analysis. Furthermore, partial least-squares discriminant analysis revealed a pairwise discrimination between the raw material group and pile-fermentation process groups or the final product group, and 48 differential metabolites with variable importance in the projection value greater than 1 were identified, which was confirmed by the subsequent hierarchical cluster analysis. These results highlight our current understanding of the exact changing process of the bioactive compounds during the pile fermentation, and the global change of these bioactive compounds provides the special flavor, taste, and health promoting effects of ripened pu-erh tea.