The Jinjiwo copper deposit is located in the Jiurui ore district of the Middle-Lower Yangtze Metallogenic Belt. The deposit has stratiform orebodies hosted by Late Carboniferous carbonate units. Pyrite is the dominant metallic mineral in the ores. Here we report on an integrated study on the microfabrics, Raman spectroscopy, in-situ LA-(MC-)ICP-MS trace element and sulfur isotope of pyrite, with a view to understand the geochemical variation, genesis of copper mineralization and ore-forming process. Textural observations suggested four types of pyrite corresponding to three metallogenic episodes: syngenetic sedimentation (PyI), metamorphism or deformation (PyII), and skarn-hydrothermal mineralization including the late skarn stage (PyIII) and hydrothermal stage (PyIV). Raman spectra of pyrite reveal subtle differences in band position and widths (FWHM) and display the increasing formation temperature of from PyI, through PyIV and PyIII, to PyII. Colloform and laminated pyrite (PyI) share similarities in behavior of pairs of elements and have low Co/Ni ratios, and the former contains the highest concentrations of Bi, Cu, Pb, Zn, Ag, Au, Mn that suggest rapid precipitation from highly saturated fluids. PyII shows high Co, Ni and As concentrations and Co/Ni ratios of 0.03 to 6.19. PyIII and PyIV have greatly varying Co/Ni ratios of 1.07 to 29 and typically low Au concentrations, suggesting a hydrothermal source. PyIII is rich in Co and Se, but is depleted in As, Cu, Pb, Zn, Ag, and Au in comparison with PyIV. There are two kinds of sulfur: one is that δ34S values are near zero, suggesting that the pyrite sulfur in the ores was derived from a mixed source in deep crust, and the other is that δ34S values are less than −39.1‰, indicating the sedimentary pyrite sulfur was originated from bacterial sulfate reduction. The combined textural and compositional data of pyrite suggest that the formation of the Jinjiwo copper deposit might have recorded the submarine exhalation sedimentation and the Mesozoic tectonic transition-deformation and hydrothermal overprint.