The oxygen reduction reaction (ORR) by the nitrogen-doped fullerene (C59N) catalyst demonstrates an excellent activity in hydrogen fuel cells. However, the intermediates and catalytic active sites in pathways have not been directly characterized, hindering the understanding of the enhanced activity mechanism for ORR on C59N. By taking the inhomogeneity of spatially confined plasmon (SCP) into account, we theoretically propose that the high-resolution tip-enhanced Raman scattering (TERS) can effectively identify different intermediate configurations of ORR on C59N. With the modulation of the focused SCP center position, vibrational modes that are directly related to site-specific O2−C59N interactions in ORR can be lighted up and then selected out by TERS spectra. Furthermore, the vibration-resolved TERS images for the selected modes of different intermediate configurations give spatial hot spot around the adsorption site, providing the in-situ details of catalytic active sites of ORR on C59N. These findings serve as good references for future high-resolution TERS experiments on probing catalytic systems at the molecular scale.