With shallow mineral resources gradually being depleted, deep-earth exploration has become imperative for ensuring national resource security. Against this backdrop, the precise three-dimensional characterization of deep geological structures and metallogenic systems, aiming to achieve “transparent ore districts,” has emerged as a key approach of deep mineral exploration. Owing to its sensitivity to both conductive mineralized bodies and resistive ore-controlling structures, three-dimensional electromagnetic surveying has gradually been established as a pivotal geophysical tool for imaging deep metallogenic systems and enabling “transparent ore districts.” First, the urgency of detailed surveys, driven by strategic demand for breakthroughs in deep mineral exploration, was outlined. Next, the characteristics and recent advances of mainstream techniques, including magnetotellurics (MT), controlled-source audio-frequency magnetotellurics (CSAMT), and the transient electromagnetic method (TEM), were summarized. Particular emphasis was placed on key advances in 3D forward modeling and inversion algorithms, including efficiency optimization using the adjoint-state method and joint inversion constrained by multi-source information. The practical effectiveness of 3D EM technology in deep structural characterization and mineral prospecting prediction was demonstrated through representative case studies in China and abroad. Finally, the bottlenecks existing in current aspects such as complex environmental noise suppression, extraction of deep weak signals, inversion multi-solutionality, and computational efficiency were deeply analyzed. The future development trend towards intelligence, integration, and efficiency was also prospected. It was believed that the continuous innovation and deep integration of three-dimensional electromagnetic detection technology is the key to achieving “transparency” in mining areas and promoting breakthroughs in deep mineral resource exploration. Based on this, a three-dimensional electromagnetic detection operational technology route for complex environments and deep targets was proposed, which provides a reference for transparent modeling of mining areas and deep-level prospecting prediction.