The rational design of non-Pt oxygen reduction reaction (ORR) catalysts and catalyst layers in fuel cells is largely impeded by insufficient knowledge of triple-phase boundaries (TPBs) in the micropore and mesopore ranges. Here, we developed a size-sensitive molecular probe method to resolve the TPB of Fe/N/C catalyst layers in these size ranges. More than 70% of the ORR activity was found to be contributed by the 0.8- to 2.0-nanometer micropores of Fe/N/C catalysts, even at a low micropore area fraction of 29%. Acid-alkaline interactions at the catalyst-polyelectrolyte interface deactivate the active sites in mesopores and macropores, resulting in inactive TPBs, leaving micropores without the interaction as the active TPBs. The concept of active and inactive TPBs provides a previously unidentified design principle for non-Pt catalyst and catalyst layers in fuel cells.