Ionic liquids (ILs) have been explored as a surface modification strategy to promote the oxygen reduction reaction (ORR) on Pt/C and their chemical structures were identified to have strong influence on the ORR activities. To better understand the roles of anion and cation of ILs on the catalytic reaction, two cations ([MTBD]+ and [bmim]+) were paired with three anions ([TFSI]−, [beti]−, and [C4F9SO3]−) to form various IL structures. By systematically varying the IL combinations and studying their effects on the electrochemical behaviors, such as electrochemical surface area and specific ORR activities, it was found that cation structure had a higher influence than anion, and the impact of the [MTBD]+ series was stronger than the [bmim]+ series. In addition to the investigation in the half-cell, studies were also extended to the membrane electrode assembly (MEA). Considerable performance enhancements were demonstrated in both the kinetic region and high current density region with the aid of IL. This work suggests that IL modification can provide a complementary approach to improve the performance of proton exchange membrane fuel cells.