The tectonic background and sedimentary environment during the transition period from the Ordovician to Silurian have been widely studied by many scholars. This study focuses on the Upper Ordovician Wufeng Formation and Lower Silurian Longmaxi Formation in the Bajiaokou profile at the southern margin of the Qinling Orogenic Belt in southern China. In order to study the aggregation mechanism of organic matter, geochemical proxies were proposed, including redox proxies (V, V/Al, U, U/Al, Mo, and Mo/Al), paleoproductivity proxies (P, P/Ti, Ba, Ba/Al, and SiXS), paleoclimate proxies (CIA), and terrigenous flux proxies (Al, Zr, and Zr/Al). In addition, Al-Co[EF] × Mn[EF] is used to provide information on paleoenvironmental parameters such as watermass restriction conditions. The redox proxies show that the Wufeng-Longmaxi shale is mainly accumulated under oxic-dysoxic conditions. During the shale deposition period of Wufeng-Longmaxi formations, the marine surface primary productivity in the southern Qinling area is generally low to moderate. The paleoclimate proxies show that from the Late Ordovician to the Early Silurian the southern Qinling area generally had a warm and humid climate. The upwelling current is widely developed in the northern margin of the Sichuan Basin and the southern margin of the Qinling area. Although the upwelling current was highly developed during the deposition of the Wufeng Formation in the Bajiaokou profile, the concentrated accumulation of a large amount of volcanic ash resulted in the low primary productivity of the ocean. During the sedimentary period of the Longmaxi Formation in the Bajiaokou profile, the development of seasonal upwelling currents and a small amount of volcanic ash supply increased the primary productivity to moderate, which provided a good material basis for the enrichment of organic matter, but the high detritus flux and the water body condition of oxic-dysoxic resulted in the slight enrichment of organic matter.