Depicting metalliferous fluid flows in sedimentary basins has a remarkable implication for understanding the formation and evolution of organic-rich sediments. The Middle-Upper Yangtze region in South China hosts voluminous gaseous hydrocarbons and MVT-type ZnPb deposits. Natural gases are mainly distributed in the Sichuan Basin, yet ZnPb deposits are found in surrounding regions of the basin. Such a unique distribution pattern implies that the interplay between metalliferous fluids and organic-rich sediments may be extensive in the boundary of these two types of deposits. A typical Ordovician/Silurian (Wufeng/Longmaxi formations) organic-rich black shale outcrop occurs in the eastern boundary of the Sichuan Basin. Pyrites are frequently distributed across this section, providing an ideal opportunity to investigate features of metalliferous fluids and their potential impacts on organic-rich sediments. Pyrites associated with high-angle carbonate veinlets are recognized in the studied area, and this group of pyrites (“Group 2”) commonly display planar-laminated morphologies, moderate δ34S values (0.78 ‰–8.86 ‰), and elevated trace metal contents (Ni, Pb, Mn, Mo, Tl, and REE) than those not associated with carbonate veinlets. These features suggest that this group of pyrites may be precipitated via local metalliferous fluid flows. Besides, pyrites with relatively lower trace metal contents can be further divided into two groups, including a group of euhedral/subhedral pyrites with more depleted δ34S values (−18.06 ‰ – -1.15 ‰; “Group 1”) and a group of planar-laminated/cubic pyrites with enriched δ34S values (10.55 ‰–37.62 ‰; “Group 3”). Pyrites of Group 1 and Group 3 may be formed via bacterial sulfate reduction (BSR) and thermochemical sulfate reduction (TSR), respectively. The discovery of fluid-related, trace-metal-enriched pyrites implies that fluid circulation within organic-rich black shales has the potential to remobilize, transport, and re-deposit trace metals. Besides, metalliferous fluid may also promote organic matter maturation within the Sichuan Basin. The outcomes of this study, combined with previous findings of metalliferous fluid flows in the center of the basin and ZnPb mineralization belts surrounding the basin, imply that a widespread Ediacaran-Palaeozoic fluid circulation system may exist in the Middle-Upper Yangtze region.