The Weibao copper–lead–zinc skarn deposit is located in the northern East Kunlun terrane, NW China. Igneous intrusions in this deposit consist of barren diorite porphyry (U–Pb zircon age of 232.0 ± 2.0 Ma) and ore-bearing quartz diorite and pyroxene diorite (U–Pb zircon ages of 223.3 ± 1.5 and 224.6 ± 2.9 Ma, respectively). Whole-rock major and trace element and accessory mineral (zircon and apatite) composition from these intrusions are studied to examine the different geochemical characteristics of ore-bearing and barren intrusions. Compared to the barren diorite porphyry, the ore-bearing intrusions have higher Ce⁴⁺/Ce³⁺ ratios of zircon and lower Mn contents of apatite, indicating higher oxidation state. Besides, apatite from the ore-bearing intrusions shows higher Cl contents and lower F/Cl ratios. These characteristics collectively suggest the higher productivity of ore-bearing quartz diorite and pyroxene diorite. When compared with ore-bearing intrusions from global porphyry Cu deposits, those from Cu–Pb–Zn skarn deposits display lower Ce⁴⁺/Ce³⁺ and Eu_N/Eu_N* ratios of zircon and lower Cl and higher F/Cl ratios of apatite. We conclude that these differences reflect a general geochemical feature, and that zircon and apatite composition is a sensitive tool to infer economic potential of magmas and the resulting mineralization types in intrusion-related exploration targets.