The Permian Chert Event is of great significance to understanding the geological evolution of the entire Permian; however, the origin of widespread chert formation is debated. We report new geochemical data from deep-marine siliceous rocks of the upper Permian Da-long Formation, Lower Yangtze region, southeastern China. Their geochemical results show that these thin-bedded siliceous rocks have a clear biologic origin, with rare to no evidence of hydrothermal influence. The values of Al/(Al + Fe + Mn) and Eu/Eu* are 0.60–0.84 (mean = 0.72) and 0.45–1.08 (mean = 0.77), respectively, and Mn/Ti ratios are relatively low (mean = 0.72). The correlations of La_N/ CeN, La_N/ Yb_N, and Fe₂O₃/ TiO₂ with Al₂O₃/(Al₂O₃ + Fe₂O₃), along with the Ce anomaly, indicate that the Da-long siliceous rocks were deposited at a transitional zone between a continental margin and the open ocean; i.e., relatively close to terrestrial sediment input and far from hydrothermal activity. The accumulation of chert is related to its unique paleogeographic location in an equatorial setting with many submarine paleo-highlands. Intense upwelling and frequent local volcanism are the main factors that promoted the development of siliceous rocks in the studied area. Ocean acidification triggered by large-scale volcanism (Large Igneous Province) during the late Permian led to extensive silica precipitation and preservation.