The Gutaishan is an important intrusion-related gold (Au) deposit within the Jiangnan Orogen in South China. It is characterized by the superposition of multistage alteration/mineralization that occur as (I) pre-ore barren quartz veining, (II) early-ore quartz-dolomite-pyrite-arsenopyrite mineralization, (III) late-ore quartz-dolomite-native gold-pyrite-arsenopyrite-stibnite mineralization, and (IV) post-ore quartz-dolomite ± pyrite veining. The main gold hosts of the Gutaishan deposit are the Stage II to IV pyrites, but these have different trace-element compositions and occurrences. For example, from Stages II to III, there are variations in Se, Co, and Bi that suggest increasing oxygen fugacity (fO2), which then decreases slightly from Stage III to IV. The Stage II fine-grained pyrite has high As contents that may have resulted from rapid pyrite precipitation, whereas the high As contents in the Stage IV pyrite (coupled with the absence of sericite in Stage IV) may be the result of neutralization of acidic ore fluids. The Gutaishan ore-related pyrites have similar trace element compositions to those of typical hydrothermal pyrite, such as Se/Te (22.08–78.96), low Co/Ni (0.03–0.95), and a wide Ni range (0.195–892 ppm), which implies a major sedimentary contribution. This study integrates information on regional extensional setting, published H–O–S–Pb data, and an analysis of the close space–time relationship between the Gutaishan and Baimashan granites. The existence of a genetic link between Gutaishan Au mineralization and the emplacement of Late Triassic Baimashan granite is proposed, in addition to an amount of sedimentary input to the Gutaishan. These results reveal that the intrusion-related gold deposits in the Jiangnan Orogen have considerable exploration potential.