Silica accumulation in the Yangtze Sea during the Ordovician–Silurian (O–S) transition appears to have coincided with global climatic fluctuations, widespread upwelling, and volcanism. There is a need to further evaluate their respective contributions to silica deposition and potential relationships among these factors. The current study selected siliceous deposits in the Wufeng and Longmaxi Formations from four sections spanning the inner to outer Yangtze Sea, South China, to gain a deeper understanding of the climatic and oceanographic evolution associated with silica enrichment. Al/(Al + Fe + Mn) values, the presence of radiolarians, and Si isotope values of samples recovered from the investigated shale successions offer compelling evidence that the silica is largely of biogenic origin with some terrigenous contributions. Further, various productivity and redox proxies suggest that biogenic silica (BSi) accumulated under conditions of enhanced marine productivity and anoxic bottom water conditions. Hg/TOC and Zr/Al2O3 profiles suggest intermittent volcanism during the BSi deposition in the Yangtze Sea. However, the lack of correlation between BSi and Hg/TOC values indicates that volcanic iron fertilization was not responsible for BSi accumulation. Instead, most BSi-rich samples are dominated by low MnEF × CoEF values (<0.5), consistent with BSi deposited in modern upwelling settings. Hydrographic reconstruction based on Mo–U covariation indicates a more open water setting in the outer Yangtze Sea, while the coeval inner Yangtze Sea was relatively restricted. Therefore, upwelling events appear to have been more vigorous in the outer Yangtze Sea. Published and new Chemical Index of Alteration (CIA), BSi, and MnEF × CoEF data for the Wufeng and Longmaxi Formations across the inner to outer Yangtze Sea demonstrate that temporal and spatial variations of BSi were controlled by climate-driven upwelling. In particular, cool-water upwelling contemporaneous with Hirnantian glaciation may have been responsible for the establishment of the cool-water fauna of the shallow-water Guanyinqiao Bed and enhanced silica deposition in deeper water. Moreover, a moderate negative relationship between compiled CIA and BSi contents suggests that enhanced upwelling driving BSi accumulation appears to have been favored during cooling events. Integrated analysis of BSi deposits of the Laurentia and Baltica continental margins further suggests that BSi accumulation on continental margins during the O–S transition was primarily influenced by global cooling. Therefore, we suggest that wind patterns or/and thermohaline circulation, influenced by climate fluctuations, induced widespread cold water upwelling events during the O–S transition. Moreover, elevated BSi production diluted accumulating OM resulting in the observed parabolic relationship of BSi and TOC.