Abstract: In order to achieve a breakthrough in deep prospecting and expand the scale of ore bodies in marine sedimentary manganese deposit of Northern Santonggou in Qinghai Province, the authors adopted geophysical prospecting work such as wide-field electromagnetic method and audio frequency magnetotelluric method. At present, the production practice is still based on one-dimensional and two-dimensional inversion to interpret the geological results, and it may lead to insufficient approximation of the inversion results with the actual geological conditions, which will directly affect the subsequent prospecting results. The tectonic characteristics of the mining area, the deep burial of the strata and rock mass, and the deep electrical characteristics of the ore bearing rock series were described in this paper, based on the 3D inversion results of the wide-field electromagnetic method and the known geological and drilling facts. The results show that the sedimentary center of the mining area has not been destroyed by the intrusive rock mass using 3D inversion model, and has the characteristics of intact preservation along the strike and large thickness in the deep. A number of characteristic horizons of manganese bearing rock series with alternating distribution of high and low resistivity existe in its core, which has good deep prospecting potential.