<p>As the proton transport channel and binder within the catalytic layer (CL), the physicochemical properties of the ionomer can affect the CL microstructure and performance of the membrane electrode assembly. In this paper, we select ionomers with different side-chain lengths and investigate the effects of the side-chain structure and content of the ionomers on the performance of membrane electrode assembly (MEA). Electrochemical tests show that at a mass ratio of 10 wt.% of ionomer/Ir (I/Ir), long-side-chain (LSC) ionomer exhibits the best performance (2.141 V@2.00 A/cm², while short-side-chain (SSC) ionomer is 2.208 V@2.00 A/cm²). The MEA containing LSC ionomer shows better electrochemical performance than the SSC at the same I/Ir mass ratio, especially at high current density. The MEA containing LSC ionomer has a larger average pore size and porosity, which indicates that it may have better mass-transfer properties. From the analysis of voltage loss, it can be seen that LSC ionomers have a smaller ohmic impedance and mass transfer resistance than SSC ionomers. In conclusion, LSC ionomers are more conducive to water-gas transport, which can provide excellent water electrolysis performance. This article focuses on the optimization of ionomer side chains and content, which can enhance PEM water electrolysis performance at lower cost.</p>