The causes of the large‐scale and intense magmatism in South China and its coeval metallogenic processes in the Mesozoic have been debated, due partly to the lack of a high‐resolution crustal model. In this study, we deploy ∼500 nodal seismometers around the Nanling metallogenic belt in South China, including one linear array across the metallogenic belt and one 2D array around the Fankou ore deposit: a deposit that hosts large amounts of lead and zinc in China. The derivation of the Moho and the intracrustal structures with receiver function imaging using the linear array was conducted in a separate study. Here, we focus mainly on the shallow shear wavespeed structure in the upper crust (from the surface to about 8 km depth) using ambient noise tomography with the 2D array data. We find low‐shear wavespeed anomalies () associated with a basin down to about 3.0 km and several high‐shear wavespeed anomalies () below 6.0 km adjacent to the Fankou ore deposit, which we interpret as the crystallized igneous intrusions in the Mesozoic. Gravity modeling shows that the high density anomaly derived using the wavespeed model is required to improve the data fitting. Considering the temperature derived from a typical geothermal gradient is insufficient for mineralization, we propose that the fluid and heat brought by the igneous intrusion might contribute to the mineral concentration of the Fankou ore deposit. This observation is consistent with geochemical and petrological evidence of diabase and quartz diorite veins in the study region. The experiment shows that ambient noise tomography using dense nodal arrays has the potential in resolving the favorable conditions for ore formation and may play a role in future ore exploration.