Many lakes exist in southeastern Badain Jaran Desert and its hinterland, including 110 perennial lakes and some seasonal or extinct lakes. Geomorphological, sedimentological, and bioglyph evidence obtained from field investigations on Badain Jaran Desert lake group, alongside measurements and dating performed on lake relic, prove that these lakes expanded while the climate was relatively wet during early and middle Holocene. The dating results suggest that the pan-lake period of the Badain Jaran Desert began at 10 cal kyr BP, before which the limnic peat period occurred(11–10 cal kyr BP). Many lakes reached their maximal water-level during 8.6–6.3 cal kyr BP and retreated or dried up in the late Holocene(about 3.5–0 cal kyr BP). During that period, the precipitation at Badain Jaran Desert may have reached 200 mm yr~(-1) for 7.7–5.3 cal kyr BP, inferred from both the age and precipitation rate of calcareous root tubes. The water balance calculation shows that wetter and warmer climate and the increase of underground water recharge were key factors in maintaining and developing the lake group at both centennial and millennial time scales. Furthermore, lake surface expansion and the increasing fresh water availability set the background for the prosperous prehistoric culture. Many lakes exist in southeastern Badain Jaran Desert and its hinterland, including 110 perennial lakes and some seasonal or extinct lakes. Geomorphological, sedimentological, and bioglyph evidence obtained from field investigations on Badain Jaran Desert lake group, alongside measurements and dating performed on lake relic, prove that these lakes expanded while the climate was more wet during early and middle Holocene. The dating results suggest that the pan-lake period of the Badain Jaran Desert began at 10 cal kyr BP, before which the limnic peat period occurred (11-10 cal kyr BP). Many lakes reached their maximal water-level during 8.6-6.3 cal kyr BP and retreated or dried up in the late Holocene (about 3.5-0 cal kyr BP). During that period, the precipitation at Badain Jaran Desert may have reached 200 mm yr ~ (-1) for 7.7-5.3 cal kyr BP, inferred from both the age and precipitation rate of calcareous root tubes. The water balance calculation shows that wetter and warmer c limate and the increase of underground water recharge were key factors in maintaining and developing the lake group at both centennial and millennial time scales. furthermore, lake surface expansion and the increasing fresh water availability set the background for the prosperous prehistoric culture.