A novel methodology for comparing protein structural networks (PSNs) of homologous proteins is presented here, leveraging graph spectral analysis and quantitative comparison techniques. The primary objective of this approach is to systematically explore the similarities and differences between homologous protein structures, thereby elucidating the intricate relationships between protein sequence, structure, and function. By employing a combination of network similarity score, total network dissimilarity, and Fiedler vector analysis, this method provides a robust framework for identifying subtle patterns and relationships in protein structure evolution. The insights gained from this approach will contribute significantly to our understanding of protein biology.