Application of anion exchange membrane (AEM) in fuel cell technology has attracted increasing attention in the past two decades. Compared to common fuel cell membranes such as Nafion, the alkaline working conditions of AEM allow the use of non-precious metal as electrocatalysts. Hydroxide ion conductivity is a key aspect of AEM and is mainly determined by the nanoscale membrane morphologies. Fundamental understanding of the structural and transport properties of membranes in terms of polymer architectures is crucial for future development of membrane-based applications. Mesoscale simulations such as dissipative particle dynamics (DPD) are very suitable to perform morphological study for the designed AEM. Here, we focus on two most popular AEM with aromatic (polyphenylene oxide, PPO) and aliphatic (polystyrene-ethylene-butylene-styrene, SEBS) backbones, where the cationic side chains are modified by hydrophobic or hydrophilic spacers. The nanostructure of the hydrated AEM and the diffusivity of ions are affected by side-chain structure and side-chain distribution. Key findings in recent investigations will be summarized.