Pu-erh tea is one of the most popular beverages in China and Southeast Asia, however, influences from fermentation and storage on its chemical profile and quality are unclear. Thus, bioactivities and metabolomes of raw (17-raw) and ripened teas (17-rip through 06-rip) were assessed using chemical methods and a UPLC-QQQ-MS-based metabolomic approach. Results evidence that chemical components and antioxidant activities of 17-rip through 06-rip were similar but lower than those of 17-raw. Subsequently, 842 metabolites were identified from 17-raw, 17-rip and 06-rip, of which 20 and 19 metabolites were biomarkers for discerning 17-rip from 17-raw and 06-rip, respectively. Between 17-raw and 17-rip, 536 differential metabolites were identified, and 17-rip contained higher levels of gallic acid, acetyl amino acids, purine alkaloids, pyrimidine alkaloids and non glycoside flavonoids and lower levels of sour compounds, quinic acid derivatives, amino acids, flavonoids glycosides, and flavan-3-ols; all of them were found to be positively but gallic acid and acetyl amino acids negatively correlated with two tested bioactivities. Between 17-rip and 06-rip, 175 differential metabolites were identified, among which alkaloids positively correlated to the two bioactivities. Overall, this study identified biomarkers distinguishing teas with different fermentation processes and storage times and different metabolites affecting their tastes and bioactivities.