The Dongguashan copper (gold) deposit in Anhui Province is one of the largest copper (gold) deposits in the Tongling ore district, which is the most important region in the Middle–Lower Yangtze River Metallogenic Belt, Eastern China. Stratiform and lamellar orebodies are the major deposit types. Pyrite and pyrrhotite from the stratiform deposit type (Py I, Po I) and lamellar deposit type (Py II, Po II) are investigated using Electron-probe Microanalyses (EPMA) and Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). Py I, Py II, Po I and Po II have high contents of Cu, Co, Au and Se, low contents of As, Pb and Zn, with Co/Ni ratios of 0.50−48.00, 4.00−45.00, 1.55−14.45 and 1.02−1.36, respectively, most of which are greater than 1 and vary widely; these characteristics are consistent with those of pyrite with a magmatic–hydrothermal origin. The higher Au/Ag and Fe/(S + As) ratios of pyrite and crystallization temperatures (286–387 °C) of hexagonal pyrrhotite indicate that the mineralization occurrs in environments with medium- to high-temperatures, high sulfur fugacity and medium-shallow depths. Therefore, we suggest that the Dongguashan copper (gold) deposit is a stratabound skarn-type ore deposit associated with magma intrusion activity during the Yanshanian Period.