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Phylogeny analysis is widely used to determine evolution, family and function of genes. Comparing to amino acid and coding nucleotide sequences, completed genomic nucleotide sequences of gene may provide much more information for phylogeny analysis. But traditional phylogeny methods based on multiple alignment are not fit to analyze completed genomic nucleotide sequences because of complexity of computation, and lack of capability to recognize long-range distinct pattern in sequence. In this study, a new phylogeny method based on 2D graphic representation model for DNA sequence is proposed to analyze completed genomic nucleotide sequence of CYP3As, one of the most important cytochrome P450 subfamilies for metabolism of drug and lipophilic organic compounds. The 2D Graphical representation model of DNA sequence applied in this article provides a simple way of viewing, sorting and comparing various gene structures, especially this model may recognize long-range distinct pattern in some degree. This phylogeny method is proven to be effective and appropriate to phylogeny analysis for completed genomic nucleotide sequence of genes.