Water solubility of PEDOT:PSS conducting polymer is achieved by PSS at the expense of disturbing the crystallinity and electron mobility of PEDOT. Recently, PEDOT crystallinity and electron mobility have been improved by treating the PEDOT:PSS aqueous solution with 1-ethyl-3-methylimidazolium- (EMIM-) based ionic liquids (IL) EMIM:X. The amount of such improvement varies drastically with the anion X coupled to EMIM cation in the IL. Herein, using umbrella-sampling molecular dynamics simulations on the aqueous solutions of a minimal model of PEDOT:PSS mixed with various EMIM:X ILs, we show that the solvation of each ion in water plays a major role in the free energies of ion binding and exchange. Anions X efficient for the improvement are weakly stabilized by hydration (i.e., hydrophobic) and prefer binding to hydrophobic PEDOT than to hydrophilic EMIM, favoring the ion exchange. In order to fulfill our design principle, a quantitative criterion based on hydration free energy proposed to select efficient hydrophobic anions X.