The Fang’an quartz-vein gold deposit is located in the eastern part of the Bengbu uplift. The eastern part of the Bengbu uplift is considered to be the western extension of the Zhaoyuan gold mineralization zone in the Jiaodong area of Shandong Province and has huge mineralization potential. The Fang’an deposit was a newly discovered, small-sized gold deposit, and the research in the area is relatively weak. In this study, samples of quartz-vein type ore were collected from the ZK141, ZK1549, and ZK1665 drill holes of the Fang’an gold deposit. Based on the study of the geological characteristics, the major and trace elements of pyrite in different stages were analyzed by electron probe microanalyzer (EPMA), to explore the compositional characteristics of pyrite, the occurrence of gold, and the source of ore-forming fluid. The studies indicate that the deposit experienced four ore-forming stages: the quartz stage, the quartz-pyrite stage, the polymetallic sulfide stage, and the carbonate stage. The pyrites are grouped into three stages, corresponding to the first three ore-forming stages. The EPMA analyses showed that the major elements of pyrite were high Fe and low S, indicating that the formation was hydrothermal. The high content of Ni indicated that the metallogenic materials were derived from between the mantle and the lower crust. The general Co/Ni ratio of >1, with an average of 5.34, indicated that the ore-forming fluid was derived from the magmatic–hydrothermal fluid and wall rock. The Fang’an gold deposit mainly contains nano-gold.