For the efficient separation of hard-to-separate organic molecule isomers, the creation of solid materials that can distinguish between isomers and selectively collect them is important. For example, in the separation of organic molecule isomers that have multiple functional groups such as hydroxy groups, the design of host molecules that allow the precise recognition of the positions and orientations of the functional groups is required. In this study, based on sulfur-bridged phenol dimer that is a partial structure of p-tert-butylthiacalixarene, an open-chain diol-type host 2 was designed and synthesized. In compound 2, two phenolic hydroxy groups were bridged with a methylene group to fix the conformation, and two alcoholic hydroxy groups were introduced for guest recognition sites. In a competitive inclusion experiment from an aqueous solution of a cis/trans mixture of 1,3-cyclohexanediol, crystals of host 2 selectively included cis-isomer. The isomer selectivity was low for the inclusion of 1,2-diol, and 1,4-diol was not included. X-ray crystallographic analysis of the inclusion complex of host 2, which predominantly included the cis-isomer of 1,3-diol, revealed that two hydroxy groups of the host form cooperative hydrogen bonds with two hydroxy groups of the guest. The results show that densely packed stable crystals can be formed by fixing the conformation of the host to construct an inclusion space and by the precise recognition of the guest functional groups complementary to the host molecule. This study provides an approach for the design of host molecules that can selectively include difficult-to-separate target molecules.