The crystal structure of ionic nanocrystals (NCs) is usually controlled through reaction temperature, according to their phase diagram. We show that when ionic NCs with different shapes, but identical crystal structures, were subjected to anion exchange reactions under ambient conditions, pseudomorphic products with different crystal systems were obtained. The shape-dependent anionic framework (surface anion sublattice and stacking pattern) of Cu2O NCs determined the crystal system of anion-exchanged products of CuxS nanocages. This method enabled us to convert a body-centered cubic lattice into either a face-centered cubic or a hexagonally close-packed lattice to form crystallographically unusual, multiply twinned structures. Subsequent cation exchange reactions produced CdS nanocages while preserving the multiply-twinned structures. A high-temperature stable phase such as wurtzite ZnS was also obtained with this method at ambient conditions.