At present, the further development of proton exchange membrane fuel cell (PEMFC) is in urgent need of commercialization. Therein, the storage of catalyst ink is a neglected but crucial topic. Undoubtedly, a structurally stable catalyst ink is more resistant to storage and suitable for commercialization. In this work, the structural stability of catalyst inks containing short-side-chain (SSC) ionomer and long-side-chain (LSC) ionomer after storage and their effects on the catalyst layer (CL) microstructure and the cell performance are investigated. The result demonstrates that the catalyst ink with LSC ionomer has better structural stability than the catalyst ink with SSC ionomer. The adsorbed ionomers on Pt/C in SSC ionomer catalyst ink increase after ink storage, resulting in increased ionomer coverage and deteriorated ionomer distribution in the CL, which makes the cell subject to higher mass transport resistance. As a result, the LSC ionomer catalyst ink after storage can achieve the initial ink properties after redispersion, while the SSC ionomer catalyst ink fails. Therefore, to promote the practical application of SSC ionomer, the ink storage should be considered.