We find that the topology of phase diagrams for block copolymer/ionic liquid (IL) blends and the scaling of the phase-separated domains are significantly influenced by the cation structure of the IL. We have varied the cation structure of bis(trifluoromethane sulfonyl)imide ILs and investigated the influence of these changes on the thermodynamics of blends with polystyrene-b-poly(methyl methacrylate). Effective chi parameters (chi(eff)) were determined and used to plot phase diagrams, where significant differences were observed, suggesting that the balance of Coulombic and van der Waals interactions was influencing the topology of the phase diagrams. The relationship between IL structure and scaling of domain spacing was also investigated. These important findings shed additional light on the thermodynamic-driven properties of IL-containing block copolymers and have practical implications for how they can be used in nanotemplating or block copolymer lithography applications.