Ionic liquids are an important component for constructing functional materials, and polyxometalate cluster anion is a promising partner for building inorganic–organic hybrid materials comprising ionic liquids. In such hybrid materials, the precise control of the molecular arrangement in the bulk structures is crucial for the emergence of characteristic functions, which can be realized by introducing an amphiphilic moiety into the ionic liquids. Here, an amphiphilic polymerizable imidazolium ionic liquid with a methacryloyl group was firstly hybridized with polyoxometalate anions of octamolybdate ([Mo8O26]4−, Mo8) and silicotungstate ([SiW12O40]4−, SiW12) to obtain inorganic–organic hybrid crystals. The polymerizable ionic liquid with a octyl chain (denoted as MAImC8) resulted in the formation of anisotropic molecular arrangements in the bulk crystal structure, which was compared with the hybrid crystals composed from the polymerizable ionic liquid without a long alkyl chain (denoted as MAIm). Rather densely packed isotropic molecular arrangements were observed in the hybrid crystals of MAIm–Mo8 and MAIm–SiW12 due to the lack of the amphiphilic moiety. On the other hand, using the amphiphilic MAImC8 cation gave rise to a honeycomb-like structure with the Mo8 anion and a layered structure with the SiW12 anion, respectively.