In this work, high performance cross-linked anion exchange membranes with hydrophobic side-chains were prepared via quaternization reaction and a simple heat treatment. The cross-linked membrane structure, the hydrophobic side-chain and the micro-phase separated morphology of membranes have synergistic effect on ion selective separation. Accordingly, the obtained membranes possess excellent ion perm-selectivity and considerable OH- flux. Especially, QPPO-C6-120 membrane exhibits the superior perm-selectivity of 76 for OH-/WO42- system and high OH- flux of 2.72 x 10(-7) mol cm(-2)S(-1) at a current density of 30 mA cm(-2). XPS and H-1 NMR confirmed the introduction of long side-chain and the thermo-crosslinking reaction. Meanwhile, the microstructure of membranes was investigated by XRD and SAXS. More importantly, a new perspective of mesoscales by combining the molecule structure with the microstructure of membranes is innovatively used to explore the ion separation mechanism.