Abstract: The method of controlled source audio frequency magnetotelluric sounding(CSAMT) is applied in the prospecting of deep structures on the southern side of the Yilite pluton in the Shenshan Fe-Cu orefield, Inner Mongolia. The results show obviously different electrical characteristics in the layers vertically. The low resistance layer is sandwiched by upper and lower layers with high resistance. According to the distribution patterns of resistivity isolines, the emplacement boundaries between strata and Yilite pluton are inferred, and two emplacement faults correlated well with regional tectonic are identified. Study reveals that the superimposed positions of such boundaries and faults are favorable for polymetallic metallogenesis.