As one of the most crucial components, the catalyst layer (CL) plays a critical role in the performance of anion exchange membrane fuel cells (AEMFCs). However, the effect of the structural evolution of ionomer binder on the micromorphology and catalytic activity of CL is yet to be clarified. In this study, pyrrolidinum and quaternary ammonium cations are attached to the polyphenylene oxide (PPO) backbone through flexible spacer units (five, seven, or nine carbon atoms) with different terminal alkyl groups. The Van der Waals force and electrostatic repulsion between the ionomer binder and catalyst are regulated through the flexible spacer units and terminal alkyl groups to alleviate the agglomeration of catalyst particles and acquire a high catalytic activity. To evaluate the electrochemical stability of the cationic groups, the alkaline stability of the ionomer binder is tested under a constant voltage to simulate the true operational environment of the fuel cells. The results reveal that the degradation of the cation groups of ionomer binder is accelerated under a constant voltage condition. This phenomenon in neglect earlier, may serve as a useful reference for the synthesis and performance enhancement of ionomer binders.