A novel gemini amphiphile bearing a rigid spacer was found to form an inclusion crystal with water in a 1:3 host-to-guest molar ratio. The host molecules can generate a hydrophobic cavity unit via intermolecular intersections between each two neighbouring molecules, which can be connected with one another at one direction, resulting in a channel finally. At the same time, one-dimensional (1D) water chains are trapped in channels by weak C-H…O, O-H…Br- and C-H…Br- interactions with the walls composed of the host molecules. These interactions and water chains, together with the alternatively arranging water chain and host molecule layer, can form a two-dimensional network in crystal, which can stabilize the crystal structure. The profound contribution of water chains to the stability of the host framework is clarified by comparisons of properties between water-held crystals and water-removed materials. Meanwhile, weak interactions are theoretically calculated and visualized by Noncovalent Interaction (NCI) analysis, and further confirmed by spectral experiment. Both experiments and calculations reveal that these weak hydrogen bonds provide a vital cohesion on the stability of crystals.