Minqin Basin, a basin locating in the lower reaches of the Shiyang River, is now covered by sand desert in large area. A huge lake, Megalake Tengger, was evidenced existing to the east of Minqin Basin. However, it is still unclear whether the Minqin Basin was covered by the Megalake Tengger. Thereafter, the spatial distribution of deep lake lacustrine sediments was analyzed by using 50 m deep sedimentary sequence of 8 hydrogeological cores based on the GIS platform. 2-3 deep lake lacustrine units with thickness ranging between 0.5 m and 32 m were recovered from most area of the northeastern Minqin Basin, and up to 4 layers at some areas. The regional stratigraphic comparison supports that a deep lake once existed in the entire basin sometime and scattered lakes at the other time. Combing the dating results of previous researches, a unified huge lake covering the northeastern Minqin Basin was supported sometime during the Late Quaternary, corresponding to the penultimate deep lake lacustrine sedimentary unit (or the 1 315 m altitude shoreline). However, the big difference among spatial distribution of deep lake lacustrine sediments at different stages likely resulted from transition westward and subsequently northward of the sedimentary center during the Late Quaternary.