Controllable ion transport through nanochannels is crucial for biological and artificial membrane systems. Covalent organic frameworks (COFs) with regular and tunable nanochannels are emerging as an ideal material platform to develop synthetic membranes for ion transport. However, ion exclusion by COF membranes remains challenging because most COF materials have large-sized nanochannels leading to nonselective transport of small ions. Here we develop ionic COF membranes (iCOFMs) to control ion transport through charged framework nanochannels, the interior surfaces of which are covered with arrayed sulfonate groups to render superior charge density. The overlap of an electrical double layer in charged nanochannels blocks the entry of co-ions, narrows their passageways, and concomitantly restrains the permeation of counterions via the charge balance. These highly charged large-sized nanochannels within the iCOFM enable ion exclusion while maintaining intrinsically high water permeability. Our results reveal possibilities for controllable ion transport based on COF membranes for water purification, ionic separation, sensing, and energy conversion.