The performance of a proton exchange membrane fuel cell (PEMFC) severely decreases as the relative humidity decreases. Herein, we present size-controlled silica (SiO2) nanoparticles in the catalyst layers (CLs) to provide sufficient water to the Nafion ionomer. It is found that the microstructure of the agglomerated CL is notably improved using the SiO2 particles with smaller diameter. In addition, as the SiO2 particle diameter decreases, both the electrochemical surface area and ohmic performance are improved, as well as the wettability, for the PEMFC application. The highest performance is achieved for the CL with the 8 nm SiO2 particle, which results in 2.93 times increased current density at 0.5 V relative to the 80 nm SiO2–containing CL, when SiO2-to-carbon ratio was fixed to 0.20. Consequently, it is more effective to improve the electrode morphology of the SiO2 CL than simply increase the SiO2 content, in order to enhance the fuel-cell performance under low relative humidity.