The invention provides a regional population structure analysis method based on clustering analysis of mitochondrial deoxyribonucleic acid (mtDNA) genetic information. Clustering analysis is conducted on the mtDNA genetic sequence information of regional population by adopting a clustering algorithm that a genetic algorithm is embedded into a k-modes model; and through studying the group distribution law and the distances among clustering centers, sample numbers of each group are counted and the population distribution density of each group is calculated, so that population structure characteristics of a selected region are analyzed; and by utilizing mtDNA sequence data of the regional population in a database and adopting an analysis method that the genetic algorithm is embedded into the k-modes model, a group structure division method of quantitative mtDNA molecular markers is given, so that the regional population structure characteristics are analyzed. The regional population structure analysis method achieves a good clustering effect, is high in reliability and is suitable for large-scale mtDNA data clustering analysis of regional groups.