Background <p>Maternally inherited, high-copy, non-recombining and fast-mutating, mitochondrial DNA (mtDNA) is exploited in anthropology to trace maternal ancestry and in genetics to reconstruct population histories and study disease susceptibility. The Han Chinese represent the largest ethnic group in the nation and are spread across the country in vast numbers, and their genetics have been extensively studied. However, the detailed population genetic background and maternal genetic structure of its Sichuan subgroup remain uncharacterized for the entire mitochondrial genome.</p> Methods <p>We applied next-generation sequencing to obtain the entire mitochondrial genome data from 266 unrelated Han participants from Sichuan province in China.</p> Results <p>A count of 262 haplotypes was detected among 266 Sichuan Han individuals, with the haplotype diversity for this group recorded at 0.9999 ± 0.0003. The neutrality test results for the Sichuan Han population yielded significantly negative values, while the mismatch distribution analysis revealed a distinct unimodal pattern. The results indicated that the Sichuan Han population possess considerable genetic diversity and likely experienced a relatively recent increase in population size. Most of the detected haplogroups belonged to typical East Asian lineages, such as D4, F1, M7, and B4. In order to characterize the Sichuan Han’s matrilineal landscape, mitogenomic information from a range of global populations was brought in as reference data. The analysis indicated that the Sichuan Han population shared close genetic relationships with other Han groups and several ethnic populations in East Asia.</p> Conclusions <p>The comprehensive analysis of Sichuan Han mitogenomes and their maternal genetic backgrounds contributes valuable data to the East Asian mtDNA reference resources and offers important guidance for forthcoming archaeological and genetic investigations.</p>