Objective East Asia harbors a vast territory, with many populations and a diversity of languages. China has 34 provincial-level administrative districts which distributed in seven geographical divisions, mainly populated by seven linguistic family-speaking populations. Previous studies have focused on the genetic history of origin, migration and fusion of East Asia populations. We collected and analyzed high-density SNP data of 5 147 individuals in the world, studied the genetic relationship and structure between East Asia populations, especially Chinese populations and other world populations from the perspective of geography and language.Methods We collected and carried out quality control of high-density SNP data of 5 147 individuals in the world. We studied the genetic structure of Chinese population. The final obtained 32 789 SNPs were statistically tested by allele frequency difference analysis. Meanwhile, we employed principal component analysis, phylogenetic tree, ancestry component analysis and D-test statistics to explore the genetic relationship between East Asia populations and other populations in the world, as well as the genetic relationship and structure of Chinese populations.Results We found that there were significant differences among East Asian, African, American and European. Chinese population can be divided into seven subgroups. The genetic clustering in different populations has a strong correlation with their geographical distribution, linguistic families and ethnic origin history.Conclusion We studied the genetic relationship and differences between Chinese population and world population, and systematically studied the genetic substructure of Chinese population. This will enrich the research foundation of population genetics and forensic genetics of East Asia population and provide data support for individualized medical work.