The boundary between the Bogda stratigraphic minor-region and its neighbor, the Yilianhabierga stratigraphic minor-region, has been in dispute for a long time, and the corresponding boundary of the two tectonic units have also been disputed. Determining the contact relationships between the lithostratigraphic units in the Bogda region is the key to answering the aforementioned scientific questions. The southern margin fault of Bogda has discovered and established in Bogda area in this study, it’s a large-scale and stable extension, belonging to the levitra strike-slip fault, which was hidden in the Tuha Basin and Junggar Basin on the south and north sides, respectively. Detailed field geological investigations and refined comparisons of previous research results show that the geologic entities of the northern and southern plate of the fault have different deformation histories, sedimentary histories, and histories of magmatic activity and tectonic evolution. Detrital zircons indicates different source compositions and geological background of contemporaneous terrigenous clastic rocks in Late Carboniferous on both sides of the fault, implying that the two sets of upper Carboniferous units belong to two sedimentary basins. It is shown that the southern margin fault of Bogda has the basic property of dividing the stratigraphic minor-region. The establishment of the southern margin fault of Bogda effectively defines the boundary between Bogda stratigraphic minor-region and the Yilianhabierga stratigraphic minor-region, new information is provided for the research of zonal stratigraphic grids.