As the D genome progenitor of common wheat, Aegilops tauschii Cosson is geographically widespread in central Eurasia. In spite of intensive global studies, the origin and population structure of Ae. tauschii from China is still ambiguous. In this work, we detected 4245 single nucleotide polymorphism across 67 Ae. tauschii accessions from whole natural habitat to re-evaluate the population structure and phylogenetic relationship. As a result, Ae. tauschii accessions from Xinjiang were consistently allocated into sublineage 1E, revealing the easternmost of the natural distribution for Ae. tauschii wild population. Unexpectedly, the accessions from Yellow River region were firstly separated from L1 to be an independent cluster, the rest of which then subdivided into sublineages 1W and 1E. In addition, Ae. tauschii in this region exhibited high F_ST values with those in Central Asia, South Asia, and Xinjiang, respectively, ranging from 0.5863 to 0.8369. These results indicate that Ae. tauschii in Yellow River region might contain individual genetic variations absent in other sublineages, which could provide excellent gene resources for improvement in common wheat. The neighbor-joining tree based on the genetic distances indicated Ae. tauschii in Yellow River region to be closely related with AY57 accession from Turkmenistan, with bootstrap value of 96%. Moreover, a synchronous flowering time was observed in AY57 accession and those in Yellow River region. These results demonstrate that the accessions in Yellow River region, as an adventive population, may be directly radiated from the southern area of Turkmenistan.