In the field of proton exchange membrane fuel cells (PEMFCs), short-side-chain (SSC) ionomers are widely considered to enhance the catalytic activity of the catalyst layer, but the mechanism of enhancement is controversial. In this work, the density functional theory (DFT) calculations and practical membrane electrode assemblies (MEAs) experiments were performed to explore the mechanism of the improved catalytic activity by SSC ionomers. The interactions between Pt representative crystal planes and low-molecular-weight model anions/PFSA fragments were investigated by DFT calculations, which revealed and divided the effects of sulfonic groups, ether groups, and side-chain structures on the adsorption energy and adsorption state. The calculations showed that the ether group of the short side chain has difficulty in interacting with the Pt surface, while the ether group around the midpoint of the long side chain could still interact with the platinum. Therefore, the ionomers having longer side chains more strongly block ORR. In practical catalyst layers, the SSC ionomer significantly improved the MEA performance especially at high voltages, and increased the rated power density by up to 56.3% compared with conventional Nafion®. This work provides a reference for developing desirable ionomers to enhance the catalytic activity of PEMFC catalyst layers.