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The Badain Jaran Desert in northern China is well known for the highest mega-dunes on Earth and unique alternating megadune-lake landform, and various formation mechanisms have been proposed. Although the relics of interdune lakes are generally considered as good palaeoenvironmental records, their evolutions and relevance to paleoenvironment change are poorly understood due to limited age control. In this study, quartz optically stimulated luminescence (OSL) and K-feldspar post-infrared infrared stimulated luminescence (pIRIR) were used to establish a chronological framework for limnic relics in order to reconstruct the evolution of interdune lakes. Our results indicate that limnic relics were deposited in MIS 5 and MIS 1, due to a lake level transgression and humid environmental condition. During the Holocene, humid conditions occurred at early to middle Holocene, immediately preceded and followed by aridity. The last 600 years have been characterized by high rates of aeolian activity. Based on field observation and luminescence ages, we propose that climate fluctuations since the Late Pleistocene have played a pivotal role in the formation of the unique landform assemblages.