Abstract The Wuyi‐Yunkai Orogen experienced a polyphase tectonomagmatism and is a key region for deciphering the alteration and thermal structure of the South China Block lithosphere. Herein, an electrical resistivity model of the lithosphere is presented via the three‐dimensional inversion of broadband (0.003–3600 s) magnetotelluric (MT) data collected along a 380‐km‐long profile comprising 62 MT sites across the Wuyi‐Yunkai Orogen, and the robustness of this model is critically evaluated through a series of sensitivity tests. The resistivity model reveals that the upper crust of the Cathaysia Block and the Wuyi‐Yunkai Orogen is dominated by high‐resistivity sedimentary cover interposed with low‐resistivity features, mainly along fault zones. High‐resistivity bodies and strong conductors in the upper crust are interpreted as magmatic rocks and tectonic mélanges, respectively. Another feature of this resistivity model is the presence of zones featuring enhanced electrical conductivity (<30 Ωm) extending from the lower crust to the upper mantle beneath the Wuyi‐Yunkai Orogen. The conductors in the lower crust are attributed to saline fluids from either the dehydration of the subducting Paleo‐Pacific slab or the regional metamorphism‐induced dehydration of sandy argillaceous rocks. In contrast, the conductors in the upper mantle are attributed to 4%–7% partial melt, which corresponds to the analyses of mantle xenoliths in South China. These conductors in the upper crust and upper mantle supply volatiles and heat to shallow geothermal systems. This work ultimately shows that the lithospheric thinning of South China is controlled mainly by mantle upwelling caused by the retreat of the subducting Paleo‐Pacific slab