The DNA sequence inter-nucleotide distance analysis method can better analyze the complete genome sequence, but it is not ideal for short genome sequence. Therefore based on inter-nucleotide distance, proposes an improved DNA sequence inter-nucleotide distance model, and combined with Euclidean distance, constructs phylogenetic tree of 70 kinds of polyoma virus genome. Through the comparison of topological structure of the obtained phylogenetic tree with results in the existing literature, finds that the obtained results are basically the same with the results computed by traditional method, and verifies the effectiveness of the proposed method.