Background <p>Cholestasis is one of the most common and devastating manifestations of liver diseases. Although bile acid (BA) metabolism disturbances have been disclosed to be related to the etiopathogenesis of cholestasis, further research is desired to obtain an in-depth understanding of cholestasis. Additionally, only a limited number of treatment approaches are available for this disorder. Pien-Tze-Huang (PTH), a traditional Chinese medicine prescription, has been extensively utilized to treat various liver diseases. However, the effects of PTH on BA-submetabolome and the underlying mechanisms haven’t been revealed.</p> Methods <p>A strategy integrating widely targeted metabolomics, untargeted proteomics, and 16S rDNA sequencing, was employed to explore the regulatory effect and the mechanisms of PTH on BA-submetabolome of lithocholic acid (LCA)-induced cholestasis mice. Furthermore, LCA-induced injury HepG2 cells were deployed for efficacy justification and the mechanism exploration.</p> Results <p>Both in vivo and in vitro assays demonstrated that PTH could protect liver against LCA-induced injury. Based on the quantitative BA-submetabolome migration and cell viability assays, 3-dehydroCA, CDCA, CA-7-S, HDCA, 3-ketocholanic acid, 7-ketoLCA, and 7,12-diketoLCA were identified as the key BA species correlating with hepatoprotective effects of PTH. Moreover, PTH restored the dramatically deflected BA-submetabolome in cholestasis mice through two different ways. On the one hand, the significantly decreased BA species can be directly supplemented during PTH administration or repaired via upregulating BA-related enzymes. On the other hand, the significantly increased BAs, such as T-<i>β</i>-MCA, TCDCA, TCA, TLCA, TMDCA, TUDCA, and TDCA, should be eliminated by the increased abundance of <i>Lactobacillaceae</i> and <i>Lactobacillus</i>.</p> Conclusions <p>PTH alleviates cholestasis by synergistically regulating certain BA species, enzymes and gut microbiota, leading to holistic BA-submetabolome shaping.</p>