Flexible porous materials generally switch their structures in response to guest removal or incorporation. However, the design of porous materials with empty shape-switchable pores remains a formidable challenge. Here, we demonstrate that the structural transition between an empty orthorhombic phase and an empty tetragonal phase in a flexible porous dodecatuple intercatenated supramolecular organic framework can be controlled cooperatively through guest incorporation and thermal treatment, thus inducing empty shape-memory nanopores. Moreover, the empty orthorhombic phase was observed to exhibit superior thermoelasticity, and the molecular-scale structural mobility could be transmitted to a macroscopic crystal shape change. The driving force of the shape-memory behaviour was elucidated in terms of potential energy. These two interconvertible empty phases with different pore shapes, that is, the orthorhombic phase with rectangular pores and the tetragonal phase with square pores, completely reject or weakly adsorb N2 at 77 K, respectively.