Palladium (Pd) nanoparticles, ionic liquids (ILs), or both are integrated with graphene sheets to serve as an electrochemical sensor for detecting various bio-species. Ascorbic acid (AA), uric acid (UA), and dopamine (DA) are used as the model analytes. To assess the effects of the constituent ions of ILs on sensing properties, various ILs, namely, EMI-SCN, EMI-DCA, BMP-DCA, BMI-PF6, EMI-NTF2, and BMP-NTF2, are investigated. The results demonstrate that the graphene/IL electrode shows superior detection sensitivity compared to those of the graphene/Pd and graphene/Pd/IL electrodes. Interestingly, the IL anions are found to play a crucial role in sensing performance. Angle-resolved X-ray photoelectron spectroscopy reveals that graphene can create an aligned cation/anion orientation in the adsorbed IL film, with the anions preferentially occupying the topmost surface, thus dominating the interaction with analytes. The graphene/EMI-SCN electrode shows the highest sensitivity among the electrodes, 1.49 μA μM-1 cm-2, and a detection limit of 0.11 μM toward DA. Even with large excesses of AA and UA, the concentration of DA can be effectively detected.