BackgroundTaxaceae, is a class of dioecious and evergreen plant with substantial economic and ecology value. At present many phytochemical analyses have been performed inTaxusplants. And various biological constituents have been isolated from variousTaxusspecies. However, the difference of compounds and antioxidant capacity of different tissues ofT. mediais not clear.ResultsIn the present study, we investigated the metabolites and antioxidant activity of four tissues ofT. media, includingT. mediabark (TB),T. mediafresh leaves (TFL),T. mediaseeds (TS),T. mediaaril (TA). In total, 808 compounds, covering 11 subclasses, were identified by using UPLC-MS/MS. Paclitaxel, the most popular anticancer compound, was found to accumulate most in TS, followed by TB, TFL and TA in order. Further analysis found that 70 key differential metabolites with VIP > 1.0 and p < 0.05, covering 8 subclasses, were screened as the key differential metabolites in four tissues. The characteristic compounds of TFL mainly included flavonoids and tanninsis. Alkaloids and phenolic acids were major characteristic compounds of TS and TB respectively. Amino acids and derivatives, organic acids, saccharides and lipids were the major characteristic compounds of TA. Additionally, based on FRAP and ABTS method, TS and TFL exhibited higher antioxidant activity than TB and TA.ConclusionThere was significant difference in metabolite content among different tissues ofT. media. TFL and TS had higher metabolites and antioxidant capacity than other tissues, indicating that TFL and TS were more suitable for the development and utilization ofT. mediain foods and drinks.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04308-6.