The mineralogical and morphological characteristics, concentration of major and trace elements, and sulfur isotopic composition of three pyrite and two coal samples in the Upper Permian high-sulfur coals from Xingren, Zhijin, and Hefeng mining area, South China, were investigated, by using optical microscopy, field emission-scanning electron microscopy in conjunction with an energy-dispersive X-ray spectrometer (FE SEM-EDS), X-ray powder diffraction (XRD), X-ray fluorescence (XRF), inductively coupled plasma mass spectrometry (ICP-MS), cold vapor atomic absorption spectrometry (CVAAS), and isotopic ratio mass spectrometer. The pyrite in Xingren and Zhijin coals mainly occurs as nodular, lens-shaped, thin-layer, and massive forms, and it occurs mainly as fine vein fillings in the Hefeng coals. Microscopically, pyrite in the coals from Xingren, Zhijin, and Hefeng mainly occurs as framboidal, cell-filling, and vein-filling forms, respectively. There is a distinct difference in X-ray powder diffractogram and diffraction data of the three pyrite samples. There is a maximum diffraction peak (2.709 A) in pyrite in the coals from Xingren and (2.707 A) in pyrite in the coals from Zhijin; however, the maximum diffraction peak is 3.343 A in pyrite in the coals from Hefeng. The average unit cell length (a0) is 5.4169 A for the Xingren pyrite, 5.4159 A for the Zhijin pyrite, and 5.4170 A for the Hefeng pyrite. The ratio of S/Fe is 2.16 for the Xingren pyrite, 2.09 for the Zhijin pyrite, and 2.01 for the Hefeng pyrite. Copper (701 μg/g), Ni (369 μg/g), and Co (29.6 μg/g) concentrated in the Hefeng pyrite. The concentration of As is 126, 19.6, and 19.1 μg/g in the Hefeng, Zhijin, and Xingren pyrite, respectively. Mercury is 11.7 μg/g in the Xingren pyrite, 2.79 μg/g in the Zhijin pyrite, and 0.512 μg/g in the Hefeng pyrite. There is a clear tendency that elements Cu, Ni, Co, Cr, Se, Mo, and As are significantly enriched in the Hefeng pyrite. Mercury is greatly enriched in the Xingren pyrite, and Zn is enriched in Zhijin pyrite. Rare earth elements and yttrium (REY) are not abundant (8.276 μg/g) in the Hefeng pyrite and are characterized by maximum positive anomaly of Eu (Eu/Eu* = 6.54). The δ34S value is −26.9 ‰ in the Xingren pyrite, +3.8 ‰ in the Zhijin pyrite, and +3.7 ‰ in the Hefeng pyrite. The trace elements in the Hefeng pyrite and coal are As (126 and 6.1 μg/g), Hg (0.512 and 0.158 μg/g), Zn (276 and 56.7 μg/g), Se (16.5 and 1.07 μg/g), Mo (45.5 and 9.93 μg/g), Cu (701 and 37.8 μg/g), Ni (369 and 16.9 μg/g), Co (29.6 and 8.63 μg/g), Sb (2.64 and 0.742 μg/g), Cd (3.49 and 0.366 μg/g), and Pb (62.8 and 33.5 μg/g), demonstrating that these potentially toxic trace elements were mainly concentrated in pyrites. The strongly positive Eu anomaly (Eu/Eu* = 6.54) in the netted pyrite vein filled in the cleats of the Hefeng coal may be the product of epigenetic hydrothermal fluid.