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In the present research, the authors measured parameters of richness, cover and importance value of ephemeral and ephemeroid plants on south-north and east-west transects in the Gurbantunggut Desert in early spring, and investigated and analyzed the microhabitats, such as terrain, geomorphology, soil physical-chemical properties and crusts. By comparison, the regional differences in the ephemeral distribution in the desert were revealed. The species of ephemeral plants in the south and center are the richest and those in the west are the poorest in the desert. The cover of ephemeral plants in the mid-south is higher than that in the north, and that in the mid-east is higher than that in the west. The response of ephemeral plants to the spatial variation of the desert habitat forms the population-habitat gradient of ephemeral plants. The characteristics are: (1) In the habitat with higher terrain, coarser textured soil with poorer sorting and correspondingly higher organic matter and lower alkali-saline contents, Carex physoides and Eremopyrum orientale are the dominant ephemeral plants; (2) In the dry habitat with lower terrain, looser textured soil, some organic matter, alkali-saline soil, and developed crust, the ephemeral plants Alyssum linifolium and Erodium oxyrrhynchum are of characteristic of drought and alkali-saline tolerance; (3) In the habitat with lower terrain, some water and more alkali-saline soil, the ephemeral plants Neotorularia torulosa and Hypecoum parviflorum being of alkali-saline tolerance are mainly developed. However, most ephemerals are distributed in a habitat order of higher terrain, some organic, and less alkali-saline soil on the above-mentioned ephemeral population-habitat gradient. The spatial gradient of variation in desert microhabitats is small, and as a whole, the physiological character of mesophytism is represented by the desert ephemerals.