The origin of the numerous lakes in the Badain Jaran Desert region has attracted much research attention, and in particular the source of the lake water is strongly debated. Numerous previous studies of the water source of these lakes have been conducted using techniques such as analyses of the stable isotope composition of lake water and the moisture content of sand layers. However no research has been conducted on the salt film present on the various microtopographies of this region, which can indicate the occurrence of sub-surface microrunoff and the water cycle of the megadunes. Based on field investigations and laboratory analyses we characterized the salt films on the unique microtopographies of the megadune areas, including salt film arc-shaped spherical terrace microtopography, linear salt film on overhanging terrace microtopography, salt-film tadpole microtopography, and salt-film needle microtopography. Most of these salt-film microtopographies were not previously recognized and understanding their origin is geomorphologically significant as well as important for understanding the water cycle of the megadunes. The formation of salt-film microtopographies in this region can be classified into four types: Weak underground runoff formed by the accumulation of atmospheric precipitation within the fine-grained layer of the vadose zone; weak surface runoff formed by the diversion to the surface of weak underground runoff; water transport caused by strong evaporation; and wind dynamics in a later stage. The occurrence of effective precipitation and the differential distribution of precipitation between coarse- and fine-grained layers are the key conditions for the formation of salt-film microtopography, and the cementation of salts is also a direct factor in its formation. The salt-film microtopography and weak runoff in this area indicate that the sand layers have a positive water balance, with residual water being available to recharge the groundwater and lake water after losses by evaporation and transpiration. The fine-grained layer is relatively enriched in water, containing more than 3% or even 5% gravity water, and the coarse-grained layer is relatively depleted, containing a small amount of adsorbed water. The formation mechanism of salt-film microtopography can be summarized as follows: Effective atmospheric precipitation -> differential distribution of infiltrated water -> emergence of coarse-grained water-poor layer and fine-grained water-rich layer -> production of underground weak runoff -> formation of surface weak runoff -> strong evaporation of surface weak runoff -> precipitation and cementation of salt -> salt film formation -> hardening of the fine-grained layer -> wind erosion -> formation of a concave coarse-grained layer -> exposure of the fine-grained layer -> formation of a salt film terrace and other microtopographies. By analyzing the chemical composition of the salt films, we found that Nb was generally enriched and Ti substantially enriched, under the extreme arid climatic conditions. Hence, these two elements can be used as new indicators of an extreme arid climatic environment. And this research will expand understanding of dune landforms and its hydrologic cycles in arid areas.