Located in the Middle-Lower Yangtze River Metallogenic Belt, Tongling represents a unique ore concentration area. The velocity structure of its shallow crust plays a crucial role in deciphering the Mesozoic metallogenic processes of the entire ore district and holds considerable value for deep mineral exploration. During 2022–2023, we deployed 57 temporary broadband stations with a minimum inter-station distance of 2-5 km in eastern Tongling. We apply the continuous records to derive a high-resolution three-dimensional shear-wave velocity structure of the upper-crust in the study region by ambient noise surface tomography. The results show that the S-wave velocity in the shallow part of Xuannan Sag is significantly lower than that of Tongling Uplift, and the boundary of S-wave velocity anomalies delineates well the occurrence of the Dingqiao–Daihui Fault, which dips southeastward and extends to a depth of ~3 km. The S-wave velocity below 1 km depth of the Tongling Uplift is higher (~3 km/s) than that of the Xuannan Sag, implying possible intrusions of large-scale granities in the Tongling uplift. These intrusions display a dome-like laccolith beneath the Xinqiao and Shizishan, and a sill-like bedrock in the southern Fenghuangshan region. The results are of great significance for understanding the metallogenic dynamic process of the Tongling ore concentration area, and also provide new evidence for the magmatic underplating model of the Middle-Lower Yangtze River Metallogenic Belt.