The supramolecular hydrogel network formed from the association of poly(ethylene glycol) and α-cyclodextrin-based polypseudorotaxanes has been successfully replicated into a silica scaffold with a three-dimensional hierarchical pore structure by using a sol–gel process. The examination of the replicas indicates that the columnar polypseudorotaxane-based nanocrystallites act as crosslinkers maintaining the supramolecular hydrogel in a water-swollen state. Depending on the poly(ethylene glycol)/α-cyclodextrin formulation and the pH value, the resulting silica materials may exhibit a pore structure comprised of large mesopores (4–10 nm) interconnected by smaller ones (2–2.5 nm) in a framework where the pore walls are made-up of a microporous corona (<1.8 nm).