Metal endowment process of the clustered SEDEX (sedimentary exhalative) deposits in the Yunkai Domain (Cathaysia Block, South China) and their genetic connection with the regional tectonics is still open to debate. As a representative syngenetic deposit hosted in the black shale, the Yunfu iron-sulfide deposit (pyrite: 200 Mt @ 35%) has the potential to evaluate the missing linkage. Herein, pyrite Re–Os age and in-situ trace elements and sulfur isotope of principal ores were employed to constrain the metal accumulation process. The laminated pyrite (Py1), with the Re–Os isochron age of 303.4 ± 6.9 Ma (MSWD = 0.15), is enriched in heterogeneous distributed trace elements and highly negative heavy sulfur composition (δ34SV-CDT, mean = − 19.82‰, n = 29, standard deviation, s.d. = 0.67). This indicates the sulfur and metal precipitation was attributed for the bacterial sulfate reduction (BSR) during rapid deposition in the anoxic-seawater column of open sea at the Late Paleozoic time. The massive pyrite (Py2) hosts evenly distributed trace elements and slightly negative sulfur compositions (δ34SV-CDT, mean = − 2.00‰, n = 5, s.d. = 0.19), interpreted as further refinement and purification from Py1. To further trace its metallogenic tectonic, one hundred thirty-six (136) detrital zircon grains from ores and host rocks were selected for U–Pb and Lu–Hf isotopic analyses. Four samples of ores and ore-enveloping successions obtain the agreed youngest U–Pb ages of ∼ 430 Ma, also containing some inherited zircon grains of ca. 1200–800 Ma and ca. 2500 Ma. They possess a distinctive εHf(t) value of + 28.9 to + 40.5 for Archean, −15 to + 20 for Proterozoic and − 46.6 to − 0.2 for Paleozoic grains, respectively. This records that the episodic magmatism, including the Archean subduction, Proterozoic back-arc basin, and Paleozoic intra-continental orogeny prior to the eventual pyrite deposition, supply with substantial provenance. As a result, these collective data support that the Yunfu deposit was formed during the Late Paleozoic sedimentary exhalative deposition and hydrothermal activity in a local depression basin on the Yunkai passive continental margin without coeval magmatism.