Protein domains serve as essential structural and functional units within proteins, with their organization largely defined by a limited set of domain architectures. Traditional structural comparison metrics like RMSD, TM-score, and GDT scores focus on protein backbones and often fail to capture the subtleties of inter-domain interactions and intradomain communication, which are crucial for diverse protein functions. Our work employs the use of protein structural network (PSN) analysis, which includes main-chain and side-chain atoms to investigate homologous domains. The PSN is a node and edge representation of amino acid residues, where an edge is defined between a pair of nodes (residues) that are within the interaction distance threshold. We examined the homologous domain pairs, in association with another homologous domain pair within and across proteins (type 1 and 2), vs. homologous domain pairs connected to structurally unrelated domains (type 2) by comparing their PSN. The study revealed significant variability in the network parameters (like degree change, hub preservation) between these types of domain comparisons. These findings may suggest mechanisms of having different domain functionality and structural integrity albeit maintaining similar structures. Furthermore, through graph spectral analysis, the networks of domain pairs in different types were studied to understand residue organization within individual domains and how the domain interaction partnership affects the domain structure and function. The network of two domains interacting permanently and transiently was also studied to reveal striking differences in their interfaces and beyond. This study would pave to better understand domain interactions in monomeric multi-domain proteins and eventually enable better homology differentiation of domains, thereby shedding light of folding of small multi-domain proteins.