Gut microflora has become a topic of interest in life sciences in the context of global systems biology, in which human biological system is viewed as 'superorganisms' involving an internal ecosystem of diverse microbiome. We conceive that multi-pathway modulations of the human gut microbial system exerted by traditional Chinese medicines (TCMs) to restore the balance of the gut ecology may account for a large portion of their effectiveness in host during treatment. Such a concept is evidenced by series of studies which have revealed an interactive relationship between gut microflora and TCM, involving the two important aspects: gut microflora-dependent drug metabolism in TCM and gut microflora-targeted modulation of physiological conditions, both of which highlight the significance of gut microflora involvement in the future TCM investigation.