The Qitianling pluton in southern Hunan, China, has spatially and genetically influenced the formation and distribution of a series of polymetallic deposits, including Xintianling, Baoshan, Huangshaping, and Furong. These deposits host a variety of tungsten- and tin-related deposits, often regarded as strategic and critical rare metals, and comprise one of the most prominent reserves globally. A thorough understanding of the structure of the Qitianling pluton is essential for insights into the development and evolution of the metallogenic system in southern Hunan. Working towards the goal of investigating regional structural features and magma emplacements model, we have generated three-dimensional (3-D) electrical resistivity models of the Qitianling pluton and its surrounding areas to upper-crustal depth using magnetotelluric (MT) data that range from 1000 Hz to 0.001 Hz. The results reveal that the upper-crust of southern Hunan is mainly characterized by high resistivity with multiple unique conductive zones. The high-resistivity anomalies (>1000 Ω·m) are interpreted to represent the Qitianling pluton. In addition, they correspond very well to a negative residual Bouguer gravity anomaly. Moreover, the morphology of the feature aligns with low-velocity obtained by modelling reflected seismic waves. Conductive anomalies (<30 Ω·m) near the sides of the pluton that extend through the upper crust likely indicate the presence of the Chenzhou-Linwu deep-seated fault system, which may have served as a pathway for the upward migration and emplacement of magma/hydrothermal fluids. Conductive features (<30 Ω·m) beneath the Qitianling pluton are inferred to represent ancient magma reservoirs where assimilation and mixing processes occurred before magma emplacement. Based on the geophysical models and the available geological data, a multi-stage magma emplacement model of the Qitianling pluton is proposed, which provides new insights into the W-Sn polymetallic mineralization system and the regional magmatic evolution within southern Hunan.