Unconventional hydrates with differently bound water molecules and related mazy intermolecular interaction networks need systematic investigation. The assembly rules, interaction analysis, and dehydration behavior can be dramatically more complicated when compared with those of common hydrates. In this work, creatine phosphate sodium (CPS) was selected as a model compound representing unconventional hydrates. The packing mode and the role of water molecules related to the dehydration mechanism were explored by the combination of experimental (diffraction, thermal, microscopy) and quantum chemistry computational (interplay visualization, binding energy calculation) methods. It was observed that in the structure of CPS heptahydrate and heminonahydrate, channel, isolated-site, and ion-associated water molecules exist simultaneously, constructing the framework via the coordination bond and hydrogen bond. The binding energy of some ion-coordinated water molecules is lower than that of hydrogen-bonded ones while that of some isolated-site water molecules is lower when compared with that of channel ones, which is counterintuitive. Moreover, the diverse types and locations of water molecules, complicated H₂O···H₂O interactions, and the trade-off between CPS···H₂O and H₂O···H₂O lead to multistage, variable, and binding-energy-independent dehydration behavior. This work sheds light on the novel structure and variable dehydration mechanism of complicated hydrate systems and inspires the particularity and further investigation of unconventional hydrates.