Phosphorus plays an important role in ensuring food security and promoting the development of high-tech industries. However, the geophysical exploration technology for deep-seated phosphate deposits still requires further development. Taking the Zhenxiong phosphate deposit in Yunnan Province as an example, this study acquired and processed electromagnetic data collected using audio-frequency magnetotellurics (AMT). The data was qualitatively analyzed and quantitatively inverted to obtain the electrical structure of the area within 1500 meters depth. Combined with the physical characteristics and discoveries from drilled boreholes, it was found that the host strata of phosphate deposits exhibit good conductivity. Therefore, we identified the continuous and conductive layers in the deep as key indicator layers for locating phosphate deposits and proposed two drilling boreholes in the core of the Yangchang anticline. Both of them intersected thick and rich phosphate deposits at both sites. This indicates that the results of AMT can provide important evidence for future exploration work in the sedimentary phosphate deposits in this area and adjacent areas.