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Intrinsically charged covalent organic frameworks (COFs) afford specific ionic nanochannels for mass transport, and thus become promising platforms to design membranes with unique selectivity. However, internal electrostatic repulsion and large-pore frameworks cause significant barriers that greatly limit membrane performances. Herein, we report a novel strategy to synchronously crystallize and upgrade cationic COF membranes by ion-pairing design. Ion-paired guest molecules are involved in electric-driven interfacial crystallization to offset the charges of the ionic monomers and host frameworks. This host-guest neutralization promotes the crystallization of compact COF membranes. Lateral dimension and charge nature of guest molecules fundamentally affect the ion-pairing efficiency. Tight encapsulation of the large-sized electronegative molecules effectually narrows the molecular sieving channels, yielding a significant elevation in membrane selectivity. The membrane rejection of organic ions with a size larger than 1.2 nm thus can be improved from below 50 % to above 85 % with a water permeance of ∼10 L m−2 h−1 bar−1. Prominently, our membranes demonstrate efficient recovery and pH-dependent release of bioactive pharmaceuticals, with a release rate that is 12 times higher in an acidic solution compared to a neutral environment. This work provides an ion-pairing strategy to regulate COF membranes for pharmaceutical industries and beyond. [Display omitted] • Ion-pairing is designed to crystallize and upgrade COF membranes. • Charged additives can be encapsulated to finely tune the COF membranes. • Encapsulation of the large electronegative molecules promotes membrane selectivity. • Ion-paired COF membranes realize the controlled release of bioactive pharmaceuticals. [ABSTRACT FROM AUTHOR]