Objective  To explore the regional differences of body anthropometric traits in the Han population.    Methods  From 2015 to 2019, thirty-one body anthropometric traits of three Han ethnic groups were measured from Nanning (Guangxi), Zhengzhou (He’nan), and Taizhou (Jiangsu). The gender and regional difference analysis of each trait, and the correlation analysis between age and traits were carried out. Based on the principal component analysis of individual data of body phenotypic traits, the traits with significant regional difference were extracted to finely describe the physical characteristics of the Han peoplpe in the three regions.    Results  Most of the anthropometric traits of the three Han populations were statistically different in gender and region, and there was a positive or negative correlation between certain traits and age. The result  of principal component analysis based on individual data showed that there were obvious regional differences in body anthropometric traits of the Han people. The difference between the Han Chinese in Guangxi (south of the Yangtze River) with He’nan (north of the Huaihe River) and Jiangsu was relatively large, and difference was relatively small between He’nan and Jiangsu Han Chinese. Meanwhile the Han Chinese in Jiangsu had its own characteristics in part of the phenotypic traits, which could be distinguished from the Han Chinese in He’nan.    Conclusion  The research on the body anthropometric traits confirmed that there were significant regional differences in Han population, and suggested that the Yangtze River might be the largest geographic barrier for the population migration and genetic exchange between the north and south population.