Molecular interaction networks offer a conceptual framework for better understanding the functional organization of cells. However, the intricacy of network complexity complicates comprehensive analysis. Here, we adopted a phylogenic stratification method combined with force-directed graph simulation to decompose the human protein-protein interaction network in a multi-dimensional manner. This network model enabled us to associate the network topological properties with evolutionary and biological implications. Our findings suggest the potential of using conceptual network frameworks to mimic the true functional organization in a living cell.