This paper proposes a two-dimension numerical representation of protein, which considers the symmetry of nucleotides in the double helix structure of the DNA sequence and the composition rule of nucleotides of the codon. Cosic’s one dimensional resonant recognition model (RRM) is a physico-mathematical model. The RRM uses signal processing method to indentify the information of protein sequence. Combined the two-dimensional numerical representation of protein with the Fourier transform theory of vector sequence, we put forward the higher-dimensional resonance recognition model (HD-RRM). The results show that the two-dimensional numerical representation proposed and the HD-RRM are effective when they are applied to distinguish the similarity of dual protein sequences.