The geothermal zone of southeast China, which is one of the country’s known geothermal zones, contains significant natural geothermal resources. To understand the formation of geothermal resources, a magnetotelluric (MT) investigation with a site spacing of 1⁻2 km was carried out around the Zhangzhou Basin. The recorded MT data were processed by robust time series and remote reference processing techniques. The data analysis results revealed that two-dimensional (2-D) modeling can be used to approximately determine the electrical structure. The joint inversions of TE and TM modes have been performed after distortion decomposition. In the inversion models, a low resistivity cap of 200⁻800 m thickness was observed, which represented the blanketing sediments composed of Quaternary and volcanic rocks of the late Jurassic period. The presence of high resistivity above a depth of 20 km indicates the granites are widely developed in the upper and middle crust. MT measurements have revealed some deep-seated high conductive zones, which were inferred to be partially melting at depth of 8⁻17 km, which is likely to be reason behind the formation of higher-temperature hot springs. The results also show that there is a shallower Moho, which indicates that the heat from the upper mantle may have a big contribution to the surface heat flow. Fractures-controlled meteoric fluid circulation is the most likely explanation for the hot springs.