The 3D structure of close polymer is constituted by the interaction of close contact couples among amino acid residues. In this paper, 3D protein structure of influenza A virus was predicted. Twenty kinds of amino acid residues were divided into four categories according to the number of close contact couples. The stable structure with minimum energy was obtained by using optimization genetic algorithm. The HNXP 3D lattice model was established to predict the 3D protein structure. It can be concluded that the two kinds of structures are significantly similar by computing the similarity.