Tongling ore district is one of the most well-known Cu-Au-Fe producing areas in China, where the mineralization is closely related to magmatism. The Shizishan magmatichydrothermal system is developed extensively in the Tongling ore district and has been well studied. Major whole-rock and trace element data comes from 34 rock samples of ore-related intrusions, microthermometry data of 32 fluid inclusion samples, trace element and REE data of 5 fluid inclusions of quartz samples, C-H-O is otopic data of 28 samples, and sulfur isotope data of 27 samples from representative deposits in the Tongling district. The Shizishan magmatic-hydrothermal system dataset probably reflects the characteristics of magmatic activities, the source and origin of ore-forming fluids and that of ore-forming materials.