Despite the absence of major Quaternary glaciations in arid Northwest China, significant climatic oscillations definitely impacted the evolution of the biota in situ. Phylogeography has grown as a discipline because it has provided explicit tools for the study of geographical subdivision among populations. But phylogeographical application for arid Northwest China has begun to blossom, which has provided evidence that aridification played a significant role in the increase of genetic diversity and species diversification. The time frame corresponds with Pleistocene climatic oscillations, which caused extreme aridity and the expansion of sandy deserts. In the Asian desert flora subkingdom and Eurasian forest subkingdom of Northwest China, the recurrent phylogeographical scenarios, identified by different case studies, broadly agree with longstanding biogeographic, floristic, and topographic concepts: (i) aridification promoted diversification and speciation of desert plants; (ii) desert expansion caused habitat fragmentation; (iii) the Altay–Tianshan Mountains included glacial refugia for plants; (iv) population expansion and recolonization from glacial refugia occurred during the postglacial period; and (v) desert plants persistence and alpine plants retreat during climate oscillations. We discuss the main phylogeographical findings in light of molecular and paleo-environmental evidence, emphasizing notable gaps in our knowledge and outlining future research perspectives for disentangling the evolutionary history of this arid region's flora.