Tin-Copper polymetallic ore is a type of typical ore that cassiterite is closely associated with sulfide minerals. In mineral processing of tin–copper polymetallic ore, flotation is generally used to recover valuable sulfide minerals, while gravity separation is used to recover cassiterite. A mine in Yunnan, China, uses the traditional “flotation–gravity separation” process to recover copper and tin but faces several problems during processing, such as an insufficient copper grade in Cu concentrate, a much higher grade of As in S concentrate, and a grade of S in Sn concentrate that exceeds the standard. A process mineralogy study was conducted, with a focus on Cu–S mixed concentrate, S concentrate, and Sn rough concentrate. It was determined that the main cause of these problems is not the liberation or size distribution of valuable minerals but the superstructure of pyrrhotite, which represents one of the most abundant minerals in the products. Based on EMPA, SEM-EDS, and XRD data, both monoclinic pyrrhotite and hexagonal pyrrhotite occurred in all samples. The abundance of different superstructures of pyrrhotite in one sample was determined by means of particle extraction and area calculation from microscopic images, and the distribution characteristics of monoclinic pyrrhotite and hexagonal pyrrhotite in the whole process were clarified. This process mineralogy study indicates that the strong magnetic hexagonal pyrrhotite mainly affects the copper recovery during flotation, and the hexagonal pyrrhotite mainly affects the recovery of cassiterite during gravity separation. Strong magnetic monoclinic pyrrhotite and weak magnetic hexagonal pyrrhotite should be fully considered in the optimization of mineral processing, and the magnetic separation of pyrrhotite should be adopted to optimize the overall environment of copper flotation and tin gravity separation.