Few studies regarding the hydrocarbon generation potential and genesis of the layered siliceous source rocks in the Mid-Permian Gufeng Formation (GFF) of the South Yellow Sea (SYS) has been conducted. The mineralogy and geochemistry of the siliceous source rocks in the GFF were studied in detail based on the borehole data of five wells located in the Lower Yangtze to South Yellow Sea area, and the element content were compared with those of the sediments in the modern upwelling area of Peru, from which the hydrocarbon generation potential of the GFF siliceous source rocks in the SYS and its origin were revealed. Geological data shows that the GFF in the SYS area is characterized by interbeds of siliceous rocks and siliceous mudstones in unequal thickness, and is a set of over-mature and slightly humic high-quality source rocks extending in the SWW-NEE direction. In terms of geochemistry, both the siliceous rocks and Peruvian upwelling deposits show enrichment in the elements that are sensitive to reduction and productivity, but relative depletion in K, Ti and Mn, and have Co×Mn value lower than 0.4, Cd/Mo value higher than 0.1, indicating their origin of upwelling on continental margin. This study shows that the enrichment of organic matter in the GFF siliceous source rocks in the SYS area is mainly controlled by high productivity and is formed in anoxic to euxinic environment with moderate retention. Compared with siliceous mudstone in the GFF, the terrigenous clastic input and Co×Mn value are lower and Zr/Rb value is higher in the siliceous rocks, which means that the upwelling intensity of the siliceous rocks during sedimentation is greater than that of siliceous mudstones. In addition, the siliceous mudstone of the GFF have higher chemical alteration index than the GFF siliceous rocks in some wells, which suggests that the paleoclimate warming is the main cause for the weakening of upwelling activity and the reduction of siliceous sediment content.