Tetrakis(permethyl-beta-cyclodextrin)-modified zinc(II) porphyrin (1) and tetra(beta-cyclodextrin)-modified zinc(II) porphyrin (2) were synthesized via "click chemistry". Intermolecular inclusion complexation of these structurally similar 1 and 2 with tetrasodium tetraphenylporphyrintetrasulfonate (3) led to formation of two distinctly different nanoarchitectures with alternate porphyrin and cyclodextrin arrays, which were proven to be network and nanorod aggregates, respectively, by using transmission electron microscopy, atomic force microscopy, and scanning electron microscopy. From the results of comparative studies in different solutions, we elucidated the mechanisms that result in nanorod to network aggregates transition, concluding that the complexation strength of porphyrin with cyclodextrin is a crucial factor to activate the potential binding sites of a molecular building block.