The interaction between the perfluorosulfonic acid (PFSA) ionomer and platinum group metal (PGM) catalyst in polymer electrolyte fuel cell (PEFC) inks is a critical issue for designing high-performance PEFC electrodes. During the ink fabrication, the complex interparticle interaction of the ink components determines the agglomerate morphology and size distribution. Among the ink components, the ionomer, which has amphiphilic in nature due to its hydrophobic backbone and the hydrophilic ionic group, mostly effective parameter for interparticle interaction. Therefore, understanding the interaction and molecular structure of ionomer is required for a high-performance catalyst layer. The backbone length of the ionomer which controls the spacing between ionic pendant groups is the main parameter of the ionomer character. In this study, the three different ionic spacing ionomers, made in the Solvay industry: Aquivion D72-25BS, Aquivion D83-24BS, and D98-25BS, were used for investigating the adsorption behavior of the catalyst ink and PEFC catalyst layer morphology. During the fabrication of PEFC ink and catalyst layer, all samples have same sulfonic acid molality to avoid the ionic clustering effect in the side chain. Ex-situ measurements were carried out to quantify the interparticle interaction and agglomerate size distribution in the PEFC ink. The dynamic lights scattering (DLS) carry out to determine the aggregation size distribution. The rheological behavior was conducted to understand the interparticle interactions and the agglomeration behavior of the inks by steady-shear and dynamic-oscillatory-shear measurements. It is noted that increasing the ionomer backbone length, which favors interaction via hydrophobic interaction on a carbon support, suppresses the agglomeration of ink components and decreases ink viscosity. The in situ electrochemical tests were carried out to figure out the relationship between ink formulation and catalyst layer morphology. It was found that the long ionomer backbone length helps to suppress the O₂ transport resistance and ORR kinetic loss by uniform distribution from ionomer backbone-carbon supports interaction.