The Tajiks, an Indo-Iranian population, are among the most ancient indigenous peoples of Central Asia. Although numerous articles on the genetics of Central Asian populations have studied the Central Asian Tajik, both the human history and genetic diversity of Chinese Tajiks remain poorly understood. This study provides the first batch of genome-wide genotyping data for over 700,000 single-nucleotide polymorphisms (SNPs), as well as mtDNA multiplex sequencing data in 64 Chinese Tajik samples from two neighbouring dialect groups (Wakhi and Selekur). We apply principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis and Fst to infer a fine-scale population genetic structure and admixture history. Our results reveal a close genetic relationship between Chinese Tajiks and Central Asian and ancient Iranians, along with a slight admixture signal from East Asian populations. Although both Chinese Tajiks and Tajikistani Tajiks showed genetic similarities across their genome-wide data, significant divergences in the maternal lineage composition suggest that ancient Tajik peoples migrated to China and intermarried with indigenous groups. Additional maternal and paternal haplogroup analysis indicates that Chinese Tajiks retained strong western Eurasian related genetic lineages, suggesting that large-scale population movement and genetic admixture accompanied this journey to the east.