This research presents underlying stratifications under the dunes in the south of the Badain Jaran Desert using ground-penetrating radar (GPR). The GPR data was processed and analyzed. Dune structures, sedimentary environment and geomorphological evolution were reconstructed by GPR data and sedimentological data. Field survey result and GPR images showed that the underlying topography was found to be underlain by platform topography in the southeast of the Badain Jaran Desert, and aeolian sand most covered on ancient lacustrine deposit layers. The GPR profile and optically stimulated luminescence (OSL) dating results represented that in the stages of MIS 5e and MIS 3, there existed last great lake periods or high lake levels in south desert, and then lacustrine deposit or calcareous cementation layers alternately deposited with aeolian sand, and shallow lakes and swamps even existed around 7 ka in parts of the study area covered by drifting sands. Consequently, the multiplex geomorphology in the Badain Jaran Desert is the result of global climatic undulation, which is not the only factor to the mega-dunes.