Bayan Obo is a well-known polymetallic deposit containing significant quantities of rare earth elements, niobium, thorium, and iron. However, the epoch in which mineralization occurred and the mineralization process are still debated due to the complex nature of its mineralization and geological evolution. Inadequate geophysical exploration has further contributed to this lack of clarity surrounding critical issues, such as the deep link between the main orebody and the eastern orebody, the form and distribution of the extensive dolomite, and the geologic structures in the area. Therefore, we implemented the time-domain controlled-source electromagnetic method (CSEM) to acquire electrical structures at depths down to 2.5 km between the Main and Eastern mines. According to the inverted resistivity structure, in conjunction with existing geological and drilling data, we classified the main lithologies and faults based on their resistivity characteristics. Overall, the mineralized carbonatite reflects high to moderately high resistivity. The mineralized carbonatite dips overall from north to south, with a maximum extension depth not exceeding 1.5 km, and its range of occurrence is controlled by nearly east–west-striking faults distributed along the bounding line between the roof and floor rocks. The Main and Eastern mines are connected at depth, but the morphology and position of the ore bodies have significantly changed due to multiple phases of tectonic activity. The electrical structure does not reveal any obvious syncline structures, further refuting the traditional view that the Bayan syncline controls ore formation.