AbstractRedox flow batteries (RFBs) based on aqueous organic electrolytes are a promising technology for safe and cost‐effective large‐scale electrical energy storage. Membrane separators are a key component in RFBs, allowing fast conduction of charge‐carrier ions but minimizing the cross‐over of redox‐active species. Here, we report the molecular engineering of amidoxime‐functionalized Polymers of Intrinsic Microporosity (AO‐PIMs) by tuning their polymer chain topology and pore architecture to optimize membrane ion transport functions. AO‐PIM membranes are integrated with three emerging aqueous organic flow battery chemistries, and the synergetic integration of ion‐selective membranes with molecular engineered organic molecules in neutral‐pH electrolytes leads to significantly enhanced cycling stability.