Three crystalline complexes were prepared by the inclusion complexation of p‐sulfonatothiacalix[4]arene (TCAS) and p‐sulfonatocalix[4]arene (CAS) with 2,2′‐dipyridinium (2‐DPD; (complexes 1 and 2, respectively), and TCAS with 4,4′‐dipyridinium (4‐DPD; complex 3). The crystal structures show that the calixarenes in 1 and 2 maintain their original cone conformation, with shallow inclusion of 2‐DPD, and assemble themselves into bi‐layer arrangements. However, the cone shape of TCAS in 3 is disrupted by 4‐DPD to assume the so‐called 1,2‐alternate conformation in the solid state, which is similar to the 1,3‐alternate case of CAS stabilized by 4‐DPD (4). The thermodynamics of this inclusion complexation were further investigated by microcalorimetric titration in aqueous solution. The obtained results indicated that the molecular binding ability and selectivity of TCAS/CAS with DPDs is entirely controlled by enthalpy gains accompanied by a smaller negative entropic change; these are discussed from the viewpoint of electrostatic, hydrogen‐bonding, π‐stacking, and van der Waals interactions, size/shape‐fit, and a desolvation effect between host and guest. The molecular selectivity for the inclusion complexation of 2‐DPD with CAS was found to be nine times greater than that of 4‐DPD with CAS. Combining the present crystal structures and thermodynamic parameters revealed that the position of the nitrogen atoms in the DPDs is the crucial factor for controlling the binding modes, molecular selectivity, conformational features, and assembly behavior of the host upon complexation with TCAS/CAS. This will help us to design large molecular assemblies possessing highly supramolecular architectures based on calixarenes by controlling exactly the guest molecules. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)