Skarn deposit is one of the main gold‐polymetallic deposits in Beiya, Yunnan, and constrained by its porphyries, structures and stratums, the favorable ore‐prospecting spaces are contact zones between intermediate‐acid rocks and carbonatite. Based on the physical characteristics of rocks, we realized the transition between target geological body and the geophysical field and extracted the useful information. Skarn iron deposits are characterized by low‐medium resistivity in contact zone, low density of porphyries, high susceptibility and high polarizability of the iron ore. Utilizing the geological and geophysical information, we analyzed ore‐controlling factors in different stages, implemented the locating of concealed skarn iron deposits, established a geophysical exploration mode, verified the validity of the study method on the periphery of the ore district and obtained favorable exploration results. We also proposed a locating and predicting method for the concealed skarn iron deposits, which is applicable to Beiya and other similar ore‐forming geological conditions.