The Nanling region is located at the intersection of the Yangtze Block and Cathaysia Block and is characterized by complex geological and tectonic processes, as well as distinct W-Sn-REE mineralization. Despite extensive research on the mineralization of W-Sn and REE deposits in the Nanling region, the factors impacting the distribution pattern of eastern tungsten and western tin deposits, as well as the mechanism of REE enrichment in the parent rocks, remain uncertain. Deep structural and tectonic variability plays a crucial role in the formation of mineral deposits in the upper crust. Information on deep structural and tectonic variability is contained in the Moho depth, Curie depth, effective elastic thickness, lithospheric density, and thermal structure derived from the processing and inversion of satellite gravity and magnetic data. In this paper, we comprehensively analyse satellite gravity and magnetic data from the Nanling region, integrating the processing and inversion results with the tectonic evolution of this region and relevant geological information. It is hypothesized that the Chenzhou–Linwu fault serves as a channel for mineral and thermal transfer in the Sn ore aggregation zone, facilitating the material transport from the deep mantle to the surface and ultimately leading to the formation of Sn-enriched granite. The collection area of tungsten ore is more weakly associated with the Chenzhou–Linwu fault, and through deep heat transfer, tungsten components are primarily concentrated in the Earth’s crust to produce W-enriched granite. The primary source of REE enrichment in the parent rocks associated with REE mineralization is predominantly derived from the felsic crust, and the rapid intrusion of deep magma resulting from the subduction and retraction of the Palaeo-Pacific Plate is a contributing factor to the contrasting enrichment of light and heavy rare-earth elements. Mineral crystalline differentiation is relatively high, leading to the formation of ore-forming parent rocks with high heavy rare-earth element contents.