Residue interaction network alignment plays an important role in the research of the relations between protein structure and its function. In this study, protein sequence information (residue matching degree) is introduced to the optimization function of MAGNA algorithm, which carries out network alignment through network topological information, and studied the influence of topological information and sequence information on the residue interaction network alignment. Then, an SI-MAGNA algorithm suitable for residue interaction network alignment is proposed. The experiment showed that SI-MAGNA algorithm has higher accuracy EC (edge correctness) compared with the classical alignment methods (GRAAL, MI-GRAAL, MAGNA, and CytoGEDEVO) based on network topological information. At last, using SI-MAGNA algorithm to align and analyze the residue interaction networks of biological homologous proteins from different heat-resistance temperatures, the influence of protein structure on the thermal stability is studied.