The uranium deposit of the Early Cretaceous Xiangshan caldera (southeast China) represents the world's third-largest volcanogenic uranium deposit. While the hydrothermal system defines uranium mineralization in shallow volcanic-intrusive complexes, we argue that the underlying magmatic system, identified in magnetotelluric data from the Xiangshan deposit, is equally crucial in controlling the origin and migration of ore-forming fluids and driving uranium element transport. As imaged by a three-dimensional resistivity model, a volcanic conduit containing ~4% saline fluid underlies the Xiangshan peak, interpreted to control the formation of alkali fluids that aid the early alkaline uranium mineralization. A deep-seated intrusion also imaged beneath the northwestern Xiangshan caldera likely facilitates the formation of later acidic uranium mineralization and provides the requisite heat flux. Its enhanced conductivity is attributed to graphite liberalization along grain boundaries caused by CO2-bearing volatiles upwelling or igneous carbon injection. The merged zone of the volcanic conduit and intrusion, which is located at a depth of ~10–15 km, functions as a high-level magma chamber. It is fed episodically by low partial melting of lower-crustal rocks and may contain significant uranium concentrations. Essentially, the transport and enrichment of uranium elements are enabled by such a vertical extensive trans-crustal magmatic system, resulting in the emplacement of the shallow volcanogenic uranium deposit. This work is a compelling example regarding the inherited structural control of the magmatic system on volcanic-related uranium metallogenesis.