South China has experienced the evolution of multiple stages of tectonic-magma-mineralization. It is rich in mineral resources and has multiple mineralization concentration areas, which constitute an important base for national economic development. In this paper, the three-dimensional electrical structure model of the northern part of Wuyi Mountain and adjacent areas is constructed by using the regional magnetotelluric array observation data acquired in south China and the three-dimensional inversion program of WSINV3DMT. The electrical characteristics of the model show that the deep electrical characteristics along the lower part of the fault zone exhibit obvious low resistivity anomalous zones. The low resistivity anomalous zones may be the response of deep and large faults or the assembling boundary of paleo-micro-continental blocks, which have obviously controlled the shallow fault structure. It is found that most of the major endogenous metal deposits in Wuyi area are located above the low resistivity anomaly zone and the edge of deep soft fluids. They have obvious distribution regularity. At the same time, they are mainly distributed in the gradient zone of ΔT polarized magnetic anomaly. Combined with the above distribution rules and characteristics, the favorable areas for prospecting can be preliminarily delineated in Wuyi area.