Abstract: Various methods are used for geothermal resource exploration, with the electromagnetic method being widely applied due to its sensitivity to temperature changes. Among these, the audio magnetotelluric (AMT) method is the most commonly used electromagnetic method in shallow geothermal resource exploration because of its high detection accuracy and substantial depth of investigation. To determine the spatial distribution characteristics of heat storage, cover layer, and heat conduction channel of a geothermal system located in a hot spring area with clear geothermal geological characteristics. Five AMT survey lines were established in the study area, followed by spatial analysis and three-dimensional inversion of the AMT data. The distribution characteristics of geothermal system were analyzed in combination with geothermal geological data in geothermal areas. The results show that: (1) The geological condition of the study area is complex, and the underground medium has the characteristics of three-dimensional electrical structure, which is suitable for three-dimensional inversion of the AMT data. (2) The three-dimensional electrlical structure characteristics of the study area show that there are 10 high-resistance anomalic bodies and 2 low-resistance anomalic bodies in the study area. The deep low-resistance anomalic bodies have a large range with the central resistivity value of approximately 5 Ω·m. (3) The distribution ranges of heat storage, cover layer, and heat conduction channel in the study area were determined. The buried depth of heat storage is 300−1500 m, with the primary cover layer of Quaternary deposits. It is found that the circulation channel of geothermal hot water is related to fault F1 and F2. These findings demonstrate that the surface AMT method for 3D prospecting can effectively reveal the distribution of geothermal energy, providing important technical support for the development and utilization of thermal areas.