The medium-sized Ergu Fe–Zn polymetallic skarn deposit is located in the central Lesser Xing’an Range, NE China. The ore bodies are mainly hosted in the contact zone between granodiorite intrusions and lower Cambrian dolomitic crystalline limestones or skarns. To reveal the magmatic influence on the mineralization, resource potential and metallogenic geodynamic process of this deposit, a systematic study of the geology, petrology, zircon U–Pb dating, element geochemistry, amphibole geochemistry and Sr–Nd–Pb–Hf isotopes of the Ergu deposit intrusives was conducted. The results show the following: (1) The major rock types in the mine area are medium-grained granodiorite and porphyritic granite, and the rock related to mineralization is medium-grained granodiorite. Zircon U–Pb dating suggests that the granodiorite and porphyritic granite formed at 181.9–183.8 Ma and 182.7 Ma, respectively. Thus, an Early Jurassic magmatic event led to the formation of the Ergu deposit. (2) The granodiorite and porphyritic granite are high-K calc-alkaline I-type granites that formed by comagmatic evolution with varying degrees of fractional crystallization and were likely derived from partial melting of the lower crust. The Ergu deposit occurred in an active continental-margin tectonic setting. (3) The high water content (5.69 wt % H2O), high oxygen fugacity (ΔFMQ = +1.75 to +1.82) and intermediate-plutonic emplacement (3.13 km) of the granodioritic magma are key factors in the formation of the Ergu deposit. The porphyry granite is characterized by high water content (>4 wt % H2O), reduced oxygen fugacity (ΔFMQ = −0.47) and shallow emplacement (<3 km).