Abstract Background Atherosclerosis (AS) is the most common cardiovascular disease (CVD), despite an overall declining incidence, AS remains a leading cause of death worldwide. The ZeXieYin formula (ZXYF), one of the thirteen formulas recorded in HuangDiNeiJin, a classical book of Traditional Chinese Medicine (TCM), has previously demonstrated efficacy in reducing blood lipids and combating AS. However, the precise mechanism by which it regulates blood lipids remains unclear. Given the close correlation between bile acid metabolism and cholesterol metabolism, it is imperative to elucidate the intrinsic mechanisms through which ZXYF treats AS. Purpose of the research This study aims to investigate the pivotal role of enterohepatic bile acid circulation in enhancing intestinal barrier function and mitigating AS by ZXYF. Materials and methods The AS model was established by subjecting male ApoE−/− mice to a high-fat diet (HFD). Moreover, to determine the impact of ZXYF on the integrity of the intestinal barrier, we quantified proinflammatory cytokines using RT-qPCR and ELISA. Additionally, we identified tight-junction proteins in the ileal tissues through IF. Finally, the intestinal flora metabolite and fecal bile acid composition were analyzed using 16S rRNA analysis, untargeted metabolomics analysis, and targeted metabolomics analysis. Results The ZXYF significantly improved dyslipidemia and alleviated the formation of arterial plaques in AS mice. Furthermore, the administration of ZXYF resulted in a concurrent reduction in circulating lipopolysaccharide (LPS) levels and downregulation of pro-inflammatory cytokine mRNA expression in the ileum. Additionally, there was an enhancement observed in the expression of tight junction proteins within the intestinal tissue of AS mice. Further studies found that ZXYF significantly elevated the total bile acids (TBA) and total cholesterol (TC) levels in the fecal of AS mice. The untargeted and targeted metabolomic analyses further revealed that ZXYF exerts regulatory effects on bile acid phenotype by decreasing secondary bile acids (SBAs) levels through modulation of gut microbiota composition, such as enrichment of Akkermansia (AKK) abundance, and inhibition of enterohepatic circulation of bile acids. ZXYF specifically increased the expression of hepatic bile acid synthesis enzymes CYP7A1 by modulating the FXR/FGF15 signaling pathway, thereby promoting enhanced de novo bile acid synthesis and facilitating cholesterol catabolic excretion. Conclusion The findings of our research indicate that ZXYF exerts a defensive role in the advancement of AS. The mechanism underlying the role of ZXYF in combating AS is closely associated with gut microbiota reshaping and regulation of enterohepatic bile acid circulation. Graphical Abstract