The metabolic interactions between human gut microbiome and green tea polyphenols (GTPs) were poorly studied. In this study, fecal and urine samples from postmenopausal female subjects taking the GTPs supplement or placebo for 12 months were analyzed by liquid chromatography-mass spectrometry-based metabolomics analysis. The GTPs-responsive metabolites were identified and characterized by structural elucidation and quantitative analysis of the metabolites contributing to the separation of control and treatment samples in the multivariate models. Major GTPs and their sulfate and glucuronide metabolites were not found in significant amounts in feces and urine. In contrast, GTPs-derived phenolic acids were identified as the robust exposure markers of GTPs, suggesting extensive microbial biotransformation of GTPs. Interestingly, GTPs decreased the levels of microbial metabolites of aromatic amino acids, including indoxyl sulfate and phenylacetylglutamine in urine and indole-3-carboxaldehyde in feces, but did not affect the levels of aromatic amino acids in feces. Other microbial metabolites, including short-chain fatty acids and secondary bile acids, were not affected by GTPs. 16S rRNA gene analysis indicated that the fecal microbiome were not changed significantly by chronic GTP. Overall, these results suggest that some enzymes in microbial metabolism of aromatic amino acids in human gut might be competitively inhibited by chronic GTP consumption.