Climatic fluctuations and aridification have combined with the environmental heterogeneity between north and south Xinjiang to shape the spatial genetic structure and demographic history of desert species in Xinjiang, China. Lycium ruthenicum offers a unique opportunity for surveying the spatial genetic structure, evolutionary history, and effect of environmental heterogeneity on local adaption and population divergence. Three cpDNA loci (psbA–trnH, psbK–psbI, and trnV) were sequenced for 238 individuals from 21 populations across the species range in Xinjiang. Median-joining networks, principal coordinate analyses (PCoA), BEAST analysis, species distribution models (SDMs), and least-cost path (LCP) analysis were integrated to investigate the spatial genetic patterns and demographic history of the species. The 21 haplotypes identified formed two clusters, corresponding to northern and southern populations according to the PCoA and median-joining network. BEAST analysis indicated the genetic divergence between the northern and southern populations began in the middle to late Pleistocene. Increased aridity may have triggered population differentiation and fragmentation; the expansions of the Gurbantunggut and Taklamakan Deserts and uplift of the Tianshan Mountains likely further isolated northern from southern populations. High levels of diversity and unique haplotypes were identified in the populations from the north slope of the Tianshan Mountains and the northwestern and southwestern Tarim Basin, which likely served as glacial refugia for the northern and southern groups, respectively. The distribution of genetic variation, SDMs, and LCP analysis indicate L. ruthenicum expanded from refugia along the edge of the Gurbantunggut and Taklamakan Deserts at the end of the last glacial maximum.