Electrochemical reactions of polymer electrolyte fuel cells occur in catalyst layers, and microscale structure of the catalyst layer is essential for the efficient transport of gas, electron, and proton. Catalyst inks as the dispersion of catalyst/carbon particles and ionomers are used to fabricate catalyst layers, and the preparation process of catalyst inks have an impact on their characteristics and eventually affects the structures of catalyst layers. Herein, we investigated the potential of nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) as tools to characterize catalyst inks. We developed an NMR-MRI combined technique to determine the self-diffusion coefficient of solvent molecules at a local region of samples selected from an MRI image. In addition, we used 19F NMR spectroscopy to examine the mobility of main and side chains of the ionomer in various compositions of water–n-propanol mixture solvent. It was found that the ionomer side-chain mobility increased by adding n-propanol to water. Furthermore, we showed that MRI was useful to observe the inhomogeneous particle concentration in the catalyst ink, which was not accessible via optical methods. The characterization techniques presented here are expected to promote fundamental understandings for preparing catalyst inks.