Crystallization conditions for producing crystal structures of p-tert-butylcalix[6]arene (TBC6) with different conformations were screened. Molecular recognition and self-assembly between the TBC6 host and the guest pyridine led to kinetic trapping and crystallization of intermediate exclusion complexes. These complexes were characterized by single-crystal X-ray diffraction, which revealed that the first-formed crystals are 11:2 polymorphic association complexes with winged-cone host conformations. The crystalline kinetic complex undergoes slow spontaneous dissolution and subsequently recrystallizes as thermodynamic inclusion complexes, namely a 1:3 pseudopolymorphic and three 1:1 polymorphic pyridine@TBC6 complexes. The crystal structure of the host–guest system can be tuned by changing the temperature and supersaturation conditions. Interaction energies were used to generate intermolecular interaction topologies during energy framework analysis, which were used to study the hierarchies of various interactional motifs and their topologies in this series of TBC6 complexes.