Early Paleozoic black organic sediments and bentonites occur widely in the craton basin within the Yangtze block and are generally believed to be genetically related to a specific tectonic setting on the cratonic boundary. However, the intimate relationship between their origins and the dynamic mechanisms are unclear, as exemplified by the genesis of the black shale series and bentonites from the Wufeng Formation during the Ordovician–Silurian transition (OST). In order to reveal the relationship between the Wufeng Formation and the convergence of the Yangtze and Cathaysia blocks (i.e., the intracontinental Kwangsian Orogeny), two stratigraphic sections respectively in Zhaotong area (Northeast Yunnan) and Puyi area (Northwestern Guizhou) that were located in the semi-restricted inner Yangtze Sea during the OST were systematically studied, on the basis of whole-rock geochemical composition, pyrite δ34S (δ34Spy), total organic carbon (TOC), stable Sr isotope, pyrite framboid size distribution and zircon U-Pb age, trace elements. The evidence shows that the paleo-oceanic environment changed significantly at the turn of the early–late Katian and formed the black shale series in the Wufeng Formation. These acritarch assemblages were formed in the transition process of the Upper Yangtze Basin from passive continental margin basin to foreland basin during this interval. Based on previous research on the genetic relationship between black shale series and plate tectonic movement, a basin-mountain evolution model suitable for South China in the Late Ordovician is presented. The two bentonites in the Wufeng Formation with U-Pb ages of 445.5 ± 0.8 Ma and 441.9 ± 2.4 Ma primarily originated from the intermediate–acid volcanic eruption during the collision and convergence between the Yangtze and Cathaysia blocks in the Late Ordovician, the provenance region probably being located in the Jiangnan orogenic belt. Thus, we believe that the appearance of the black shale series and bentonite in the Wufeng Formation at the turn of the early–late Katian may represent the initiation of basin-mountain transformation and the Kwangsian Orogeny in South China, which provides important evidence for the collision and convergence of the Yangtze and Cathaysia blocks in the Late Ordovician.