Abstract: The Badain Jaran Desert is located within the Alxa League in the western part of the Inner Mongolia Autonomous Region, China, with geographical coordinates roughly between 98° to 104° east longitude and 39° to 42° north latitude. Bordered by Mongolia to the north, the Tengger Desert to the east, the Ruoshui River basin to the west, and the Yabrai Mountains to the south, it covers a total area of approximately 49,200 square kilometers. As the third-largest desert in China, the water recharge mechanism of its surface lake clusters has long been controversial. This study employed the Audio Magnetotelluric (AMT) method to conduct systematic exploration of the desert's interior, completing geophysical surveys along six survey lines. These included one southwest-northeast profile spanning the desert region (150 km in length) and one near-north-south profile traversing the desert's core (25 km in length). These two representative profiles revealed the electrical structural characteristics of deep strata beneath lake-concentrated areas. The findings indicate: (1) Resistivity contour maps show no evidence of deep-seated faults within the 0–2 km depth range (no significant regional lateral resistivity gradient variations), suggesting the Altyn Tagh Fault does not extend into the Badain Jaran Desert; (2) Multiple localized high-resistivity anomalies (resistivity >2000 Ω·m) were identified, which, combined with surface monzogranite outcrops and geological data, are interpreted as Yanshanian magmatic intrusive bodies. This study provides new geophysical evidence for groundwater circulation patterns in arid regions.