We report the fabrication, structure, and heteropolyanion structure effect of polyoxometalate (POM)/ionic liquid (IL) supramolecular gels. These supramolecular gels exhibit ordered structures, as a result of their excellent reversible self-assembly, and they show various physicochemical properties, determined by the heteropolyanion structure effect of POM anions. Specifically, the formation of POM/IL supramolecular gels results in a highly ordered layer-shape structure, which has been calculated using X-ray powder diffraction patterns and proven by transmission electron microscopy images for the first time. When these POM/IL supramolecular gels are heated, they become viscous liquid sols, with melting isotropic drops and even flowerlike structures on microscopic scales, while it undergoes a reversible gel-sol phase transformation from gel to sol. The heteropolyanion structure effect in these two IL gels, [TBTP](5)PW10V2O40 and [TBTP](8)P2W16V2O62, on their physicochemical properties is demonstrated. The POM structures have a strong structure effect on the physicochemical properties. As the size of heteropolyanions increases, there is a significant improvement in the conductivity, thermal performance, and oxidizability, with a lower phase inversion temperature, which means that the Dawson-type compound, [TBTP](8)P2W16V2O62, has a higher conductivity, lower melting point, stronger oxidizability, and better thermal performance than the Keggin-type compound, [TBTP](5)PW10V2O40, under the same conditions.