Advances in identifying architecture of modules and elucidating their modes of action are gradually improving the decoding of complex relationships between phenotypic robustness and genotypic networks. However, approaches to detecting modules have largely focused on identifying modules in static graphs. In this review, we attempt to reveal the mechanism of polyphyletic architectural transformation based on modular boundary evolutions and different oscillating factors. With the rapid progress in probing into the detailed structural model of modular networks, flexible modular organization manifests a key adaptive balancing ability of allosterically regulating or reconstructing intermodular and intramodular states to uncover the novel biological alterations beyond engineering properties. We conclude by discussing the multipotent functional changes in modular architecture to provide insights into the dynamics of allosteric modular interactive networks and their possible applications for the treatment of diseases.