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Past geological and climatic changes have promoted shifts in both intraspecific differentiation and distribution ranges for many desert plants, though little is known about the effects of these changes specifically on spring ephemerals in Northwest China. In the present study, we aimed to survey the population structure and phylogeographic history of an endemic spring ephemeral species, Ixiolirion songaricum P. Yan in Northwest China. We sequenced the nITS and two ptDNA fragments (psbB-psbH and ycf6-psbM) for 265 individuals from 15 populations across the entire range. Eight nITS ribotypes and eleven plastid chlorotypes were identified, with three of them dominant. A significant phylogeographic structure was detected for the species in which two larger, distinct phylogeographic lineages were identified. A high proportion of the total genetic variation existed between populations and between the two lineages. The species had undergone a sudden range expansion in the late Quaternary, which might have been driven by an interglacial warm, humid climate following the largest Pleistocene glaciation period in Northwest China. The ecological niche modeling suggested the species experienced continuous shrinkage of potential range since the last interglacial, which is distinct from other desert plants. Overall, our results indicated that climate change associated with the Quaternary greatly promoted differentiation of I. songaricum. The shift in population distribution was likely driven by increasing aridity in Xinjiang during the Quaternary.