In this study, we explore the chemistry of accessory apatite and zircon as tools to monitor the petrogenetic and metallogenetic processes involved in the formation of the Wushan Cu- and Zhuxiling W (Mo)-mineralization related granodiorite porphyry. The Wushan granitoids are metaluminous with A/CNK of 0.88–1.01, and the Zhuxiling intrusions are weakly peraluminous with higher A/CNK values (1.02–1.12). The Wushan granitoids have εNd(t) values of −4.6 to −4.7, which, combined with the relatively elevated Mg# values (57–62) and adakitic features (high Sr/Y ratios of 51–60), indicate that they were derived from melting of a thickened lower crust of the Yangtze block with addition of small amounts of mantle components. Compared to the Wushan granitoids, the Zhuxiling granitoids have relatively high (87Sr/86Sr)i (0.70945–0.70951) and low εNd(t) values (−5.9 to −6.3) and zircon εHf(t) values (−3.8 to −9.0), suggesting their derivation dominantly from partial melting of the Neoproterozoic crust.The apatites from the Zhuxiling samples are characterized by relatively high MnO and FeO, variable Y and low Ce, which is consistent with the weakly peraluminous feature of whole rock chemistry. These apatites show notable depletion of Th and LREE, with a lower (La/Sm)N ratio (0.74–1.44) and (La/Yb)N ratio (6.2–17.9) relative to those of the host rock (3.04–3.61 and 19.1–23.4, respectively), suggesting early crystallization of some LREE- and Th-enriched minerals such as allanite/monazite before apatite crystallization. The steep trend of Ce/Sm versus Yb/Gd ratios shown by zircons from the Zhuxiling granitoids suggests that the crystallization of zircon is affected by the crystallization of titanite and apatite. Thus, the crystallization sequence of accessory minerals in the Zhuxiling intrusion is allanite, apatite, titanite and zircon. The apatites from the Wushan granitoids, however, show strongly LREE-enriched REE patterns with weak negative Eu anomalies, which indicate minor feldspar fractionation and mildly magmatic differentiation. The flat trend of Ce/Sm versus Yb/Gd ratios shown by zircon from the Wushan pluton indicates that its REE composition is affected by hornblende saturation.Zircon grains from the metaluminous Wushan granitoids exhibit remarkably higher Ce4+/Ce3+ ratios and weaker Eu/Eu* anomalies than those of the peraluminous Zhuxiling samples. And the apatites from the Wushan samples show higher Eu/Eu* (0.55–0.62) and lower Ce/Ce* (0.91–1.04) and MnO (0.05–0.09%) compared to those of the Zhuxiling pluton (with Eu/Eu* = 0.41–0.50, Ce/Ce* = 1.06–1.11, and MnO = 0.15–0.18%, respectively). The apatite and zircon chemistry suggest that the Cu-bearing granitoid formed at an oxygen fugacity higher than the W-bearing granitoid, which agrees with the fact that the Wushan granitoids show whole-rock Fe3+/Fe2+ ratios higher than the Zhuxiling granitoids. In addition, apatites from the Wushan intrusion show enrichment of Cl and higher F/Cl ratios compared to those of the Zhuxiling samples, suggesting that a water-rich parental magma with relatively high Cl content is favourable for copper mineralization.This case study shows that apatite and zircon chemistry could reflect the geochemical characteristics of their host rock and magma evolution. Moreover, they provide insights into the oxidation state, halogen fugacity, and magma differentiation of the magmatic system, which are key factors for mineralization. Our data suggest that magma associated with Cu mineralization is relatively oxidizing, chlorine enriched and less fractionated compared to W-bearing magma.