Proton exchange membranes (PEMs) are being used as gas separators, insulating electrodes, and proton conductors. Thus, understanding the morphological structure of a PEM is one of the important issues for the characterization of a proton exchange membrane fuel cell (PEMFC). Specifically, the variation in the ionic channel network under hydration of a PEM is a crucial issue. In this study, we characterized the variation in the ionic channel network of Nafion 112 under a hydrated condition by using a current-sensing atomic force microscope (CSAFM). We built a mini-sized PEMFC by using the Pt-coated tip of a CSAFM and a PEM coated with Pt/C on one side. The mini-sized PEMFC could detect the local proton conductivity of the ionic clusters in the PEM. We measured the local proton conductivity of ionic clusters by using a mini-sized PEM under different relative humidities. The results were characterized by using the ballistic transport model and revealed several crucial trends, such as increasing proton conductivity and proton mean free path with increasing relative humidity.