The introduction of long side chains into anion exchange membranes (AEMs) is a common strategy for improving OH− transport. However, the effect of different chemical structures of side-chain on OH− transport in poly(arylene indole piperidinium) AEMs remains unclear. This study investigates the effects of four distinct side-chain chemical structures in poly(arylene indole piperidinium) AEMs (specifically, all-carbon side chains (a-PITPC10), side chains with amino groups (a-PITPC7N3), side chains with ethoxy groups (a-PITPC7O3), and side chains with fluoro groups (a-PITPC10F21)) on OH− transport rates and mechanisms using molecular dynamics (MD) simulation methods. The simulation results show that the trend of OH− transport rate at the same hydration number is a-PITPC7N3 < a-PITPC10F21 < a-PITPC10 < a-PITPC7O3. The flexible side chains containing ether oxygen groups have a stronger ability to move, hence the segments have a higher degree of freedom of movement, which is beneficial to the construction of a favorable micro-morphology. At the same time, the cation-dipole interaction between the main chain cation and the ether oxygen group in the side chain of a-PITPC7O3 promotes the aggregation of nearby cationic groups, enlarging the overlapping area of the surrounding hydration shells, thereby facilitating the transport of OH−. Compared to a-PITPC10, in a-PITPC7N3, the strong hydrophilicity of the side chains causes water molecules to tend to disperse, and the bottleneck volume fraction occupied by ion transport channels is the largest, hindering OH− transport. Moreover, in a-PITPC10F21, the strongly hydrophobic side chains cause water molecules to aggregate excessively, forming wide ion transport channels, but their continuity is poor, which is not conducive to OH− transport. The flexible side chains in a-PITPC7O3 facilitate the uniform dispersion of water molecules in the system, forming continuous ion transport channels, which is conducive to improving OH− transport performance. Therefore, the poly(arylene indole piperidinium) AEM with ether oxygen groups (a-PITPC7O3) outperforms other side-chain structured AEMs (a-PITPC10, a-PITPC7N3, and a-PITPC10F21) in improving OH− transport.