The inclusion complex of p-sulfonatocalix[5]arene (SC5A) with N-methyl-N′-(naphthalen-2-ylmethyl)-4,4′-bipyridinium (MVNp2+) guest was successfully prepared in single-crystal form. The obtained structure shows that SC5A is significantly distorted from the common ‘cone’ conformation induced by the complexation of MVNp2+. Moreover, the crystal packing of MVNp2+⊂SC5A reveals that the SC5A hosts do not assemble into a typical bilayer array, but arrange themselves into an unseen face-to-back bis-chain. As a result, hydrophobic molecular channels are fabricated rarely by SC5A hosts. A host–guest solution study was further performed by using NMR spectroscopy and microcalorimetry, the results of which are in accordance with the above crystallographic results. The molecular binding behaviors of SC5A with N-methyl-N′-adamantane carbomethyl-4,4′-bipyridinium (MVAd2+) guest that is structurally similar to MVNp2+ but with a different side group were also studied by using NMR spectroscopy and microcalorimetry in solution, the results of which are similar to those of SC5A with MVNp2+ guest as well.