Crystals of a yttrium complex composed from deprotonated p-sulfonatothiacalix[6]arene, [{Y(H₂O)₈³⁺}₂{p-sulfonatothiacalix[6]arene^6–}]･16H₂O (I), were studied by single-crystal X-ray diffraction analysis. In the present crystal system of I, the thiacalixarene molecule maintains an 'up-down' double partial-cone conformation possessing two pseudo-thiacalix[3]arene cavities, which act as a 'molecular container' towards guest water molecules. Interestingly, the aquated yttrium center does not directly coordinate to the thiacalixarene sulfonate groups. In contrast, the aquated yttrium cations act as a connector to the thiacalixarene molecules to establish a one-dimensional hydrogen-bonded polymer by hydrogen bonding between the thiacalixarene molecules and the yttrium cations. The extended structure of the complex forms a supramolecular assembly via mutually supporting intermolecular π−π stacking, S−π interactions, and hydrogen bonding between two differently oriented polymers.