Pyrrhotite is a potential source of S2− for the sulfide precipitation of nonferrous metal ions in hydrometallurgy and waste water treatment. In this study, different pyrrhotite crystals were prepared using zero-valent iron and sulfur to determine the effects of the pyrrhotite's structure on the sulfide precipitation of copper ions. The results indicate that the sulfide precipitation of copper ions highly depends on the crystal structure and crystallinity of pyrrhotite. Monoclinic pyrrhotite was found to be the most effective for copper sulfide precipitation, which can be used for the selective precipitation of copper ions from arsenic wastewater. More than 96% copper ions were removed with little loss of arsenic, contributing to a copper product of 20.2% Cu and 0.7% As, which can serve as raw materials of copper metallurgy. X-ray diffraction analysis showed the presence of CuS and (CuxFe1−x)S, indicating that most copper ions precipitated as CuS and some copper ions entered the FeS lattice by a lattice substitution reaction. Therefore, monoclinic pyrrhotite may provide an alternative solution for the selective precipitation of copper from arsenic wastewater.