According to reports, gut microbiota and metabolites regulate intestinal immune microenvironment. In recent years, an increasing number of studies reported that bile acids (BAs) of intestinal flora origin affects T helper cells and Treg cells. Th17 cells play a pro-inflammatory role and Treg cells usually act an immunosuppressive role. In this review, we emphatically summarized the influence and corresponding mechanism of different configurations of the LCA and DCA on intestinal Th17 cells, Treg cells and intestinal immune microenvironment. The regulation of BAs receptors G protein-coupled bile acid receptor 1 (GPBAR1/TGR5) and farnesoid X receptor (FXR) on immune cells and intestinal environment are elaborated. Furthermore, the potential clinical applications above were also concluded in three aspects. These above will help researchers better understand the effects of gut flora on the intestinal immune microenvironment via BAs and contribute to the development of new targeted drugs.