In order to study the variation, dynamic equation of DNA sequences was established by the homology in nucleotide sequences, and further evolution distance d_y(selected evolutionary distance) between species was obtained. Selected evolutionary distance d_y was calculated in 4 nucleotide substitution models, and indicated the relationship among p-distance, d-distance and Г distance d_G. According to the characteristics of dynamic equations, selection model can be transformed into a linear regression problem. Then both of the parameter b and the average substitution ratio of nucleotide each year r were obtained by the Least Square Method. Take the mitochondrial DNA sequences of 16 species for example to illustrate the new evolution distance, and then evolution trees are constructed in order to compare different evolution distance. The results indicate that the new distance d_y is an efficient evolution distance to analyze DNA sequence.