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Disentangling how climate oscillations and geographical events significantly influence plants’ genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species <i>Ulmus macrocarpa</i> is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of <i>U. macrocarpa</i> using chloroplast DNA with ecological niche modeling. The results indicated that the populations’ genetic differentiation coefficient (<i>N</i>_ST) value was significantly greater than the haplotype frequency (<i>G</i>_ST) (<i>p</i> < 0.05), suggesting that <i>U. macrocarpa</i> had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle–late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for <i>U. macrocarpa</i> during the glacial period in Northern China. Our results illuminated the demography pattern of <i>U. macrocarpa</i> and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.