AbstractObjectivesXinjiang plays a vital role in the trans‐Eurasian population migration, language diffusion, and culture and technology exchange. However, the underrepresentation of Xinjiang's genomes has hindered a more comprehensive understanding of Xinjiang's genetic structure and population history.Materials and MethodsWe collected and genotyped 70 southern Xinjiang's Kyrgyz (SXJK) individuals and combined the data with modern and ancient Eurasians published. We used allele‐frequency methods, including PCA, ADMIXTURE, f‐statistics, qpWave/qpAdm, ALDER, Treemix, and haplotype‐shared methods including shared‐IBD segments, fineSTRUCTURE, and GLOBETROTTER to unveil the fine‐scale population structure and reconstruct admixture history.ResultsWe identified genetic substructure within the SXJK population with subgroups showing different genetic affinities to West and East Eurasians. All SXJK subgroups were suggested to have close genetic relationships with surrounding Turkic‐speaking groups that is, Uyghur, Kyrgyz from north Xinjiang and Tajikistan, and Chinese Kazakh, suggesting a shared ancestry among those populations. Outgroup‐f3 and symmetrical f4 statistics showed a high genetic affinity of SXJK to present‐day Tungusic, Mongolic‐speaking populations and Ancient Northeast Asian (ANA) related groups. Allele sharing and haplotype sharing profiles revealed the east–west admixture pattern of SXJK. The qpAdm‐based admixture models showed that SXJK derived ancestry from East Eurasian (ANA and East Asian, 42.7%–83.3%) and West Eurasian (Western Steppe herders and Central Asian, 16.7%–57.3%), the recent east–west admixture event could be traced to 1000 years ago based on ALDER and GLOBETROTTER analysis.DiscussionThe high genetic affinity of SXJK to present‐day Tungusic and Mongolic‐speaking populations and short‐shared IBD segments indicated their shared common ancestry. SXJK harbored a close genetic affinity to ANA‐related populations, indicating the Northeast Asian origin of SXJK. The West and East Eurasian admixture models observed in SXJK further provided evidence of the dynamic admixture history in Xinjiang. The east–west admixture pattern and the identified ancestral makeup of SXJK suggested a genetic continuity from some Iron Age Xinjiang populations to present‐day SXJK.