With the purpose of meeting the increasing request for the mineral resources, the present exploration is shifting from the near surface layers to deeper horizons, commonly beyond traditional prospecting methods. To improve the efficiency of explorations, the authors used Controlled Source Audio-Frequency Magneto Telluric Method for the first time in this study to locate deep manganese orebody as well as its hosting structure. The V8 multifunction electrical prospecting system was applied in four CSAMT sections eastward in Shenxi, along the strike of the major manganese deposits. Interpretation of the four CSAMT sections based on a two-dimensional inversion method, combined with geological setting and physical properties of the ore-hosting rocks, shed light on the position of the ore-hosting bed, which agrees well with the results of drilling verification in encountered strata and structures. The CSAMT method thus is of the potentiality in the further exploration of similar ore deposits.