Several magmatic Ni-Cu deposits associated with Permian-Triassic mafic-ultramafic intrusions have been discovered during the last three decades in the southern part of the Central Asian Orogenic Belt, the northeastern margin of Tarim, and the margin of the North China Craton. The accurate delineations of the large resistive rock masses are crucial for locating potential ore bodies when they are located beneath rock masse. The controlled-source electromagnetic method (CSEM) is an important tool for investigating resistivity contrast in earth subsurface. In this study, we present a comprehensive example of using frequency domain CSEM survey to delineate the resistive rock masses that are related to the forming of orebody. The horizontal electric field, which is more sensitive to resistive target than the other components, is used in our study. We first built a geophysical model of the survey area based on prior confirmed geophysical and geological information. Then, both forward and inverse modeling were performed in order to assess the detectability of the resistive ore-forming rock masses in the model. Finally, this study acquired field data in the Kalatongke Ni-Cu Deposit, which is located in the Kalatongke District of the southern section of the Central Asian Orogenic Belt, and is specifically part of China’s southern Altai Orogenic Belt. The resistive ore-forming rock masses were successfully identified during the survey process and further verified by the drilling results. It was observed that both the synthetic and field examples indicated that the adopted frequency domain CSEM method successfully measured the electrical fields, and could be utilized to explore deeply buried resistive targets in future prospecting activities.