Eastern Pamirs is among the world’s highest mountains in Central Asia. The population history for this region is still unclear. To address this issue, we analyzed mitochondrial DNA (mtDNA) sequence variations in Sarikoli (n=89), Wakhi (n=67), and Kyrgyz (n=69) populations from East Pamirs in Xinjiang, China. The surrounding lowland populations, including Tajiks (n=28) from Tajikistan, Kyrgyz (n=54) and Uyghur (n=27) people from western Xinjiang, China, were also investigated for comparisons. A total of 334 mitochondrial genomes were sequenced by using Ion Torrent PGM. The mtDNA haplogroup profiles for those populations were indicated. And some novel sub-haplogroups within haplogroups D4 and H were classified. In addition to East (e.g. A – D) and West (e.g. H – K) Eurasian mtDNA haplogroups, some South Asian specific lineages (e.g. M3 and M5) were detected in most populations. Within those haplogroups, the distribution of related sub-haplogroups showed differences among those populations, suggesting a complex admixture history in Eastern Pamirs. The Bayesian Skyline plots revealed different demographic history between highlanders and their surrounding lowlanders.