The organic functionalization of polyoxometalate (POM) clusters has exhibited increasing superiority for the rational excavation and design of advanced POM-based materials. The architectures of such inorganic-organic hybrids are just like "molecular Lego" toys by virtue of the intermolecular and/or intramolecular interactions. Although numerous novel hybrids have been reported by pioneers, the relationship between organic segments and supramolecular architectures is still ambiguous. In this paper, we focus on the influence from organic bridging ligand to the structural orientation of POM hybrid materials by X-ray diffraction, molecular simulation, and energy calculation. The results indicate that rigid organic bridging ligand possesses a much stronger tendency to form intermolecular interactions than flexible ligand and can improve the electrochemical performance for hydrogen evolution reaction.