A study on the genetic polymorphisms of 29 Y-STR loci in 1?532 unrelated males of Han population in Southern Jiangxi province and its genetic relationship with other ethnic groups in China was conducted. The Y-STR loci were amplified by DNATyperTM Y29 kit, and capillary electrophoresis was carried out by 3730 genetic analyzer. Y-STR typing was carried out by GeneMapper IDX 1.4 software, and genetic data such as allele frequency and haplotype frequency of 29 Y-STR loci were calculated. Mega-X was used to construct the phylogenetic trees for the selected populations. The molecular variance analysis (AMOVA) of YHRD online tool software was used to calculate the genetic distance between Southern Jiangxi Han population and other populations, and at the same time to construct multi-dimensional scale map (MDS). After analysis, the gene diversity (GD) values of 29 Y-STR loci ranged from 0.381?5 to 0.876?6. In addition to DYS508, DYS437, DYS391 and DYS438 loci, the GD values of the other 25 gene loci were higher than 0.5. The haplotype diversity (HD) was 0.999?924, indicating that 29 Y-STR loci had high genetic polymorphism in Southern Jiangxi Han population. Compared with the Han population in other areas, the genetic distance between the Han population in Southern Jiangxi and Fujian was the closest (genetic distance Rst is 0.000?2), and that between the Han populations in Southern Jiangxi and Heilongjiang was the furthest (Rst is 0.024?9). Compared with other ethnic groups, the Han nationality in Southern Jiangxi had the closest genetic distance to the Bai nationality in Yunnan (Rst is 0.005?9), and the furthest genetic distance to the Tibetan nationality in Ganzi (Rst is 0.468?9). The results showed that the 29 Y-STR loci in this study have high genetic polymorphism in Southern Jiangxi Han population, which can meet the requirements of family investigation and forensic examination. The data obtained can provide data support for research and application of population of genetics and forensic science.