State-of-the-art proton exchange membranes (PEMs) often suffer from significantly reduced conductivity under low relative humidity, hampering their efficient application in fuel cells. Covalent organic frameworks (COFs) with pre-designable and well-defined structures hold promise to cope with the above challenge. However, fabricating defect-free, robust COF membranes proves an extremely difficult task due to the poor processability of COF materials. Herein, a bottom-up approach is developed to synthesize intrinsic proton-conducting COF (IPC-COF) nanosheets (NUS-9) in aqueous solutions via diffusion and solvent co-mediated modulation, enabling a controlled nucleation and in-plane-dominated IPC-COF growth. These nanosheets allow the facile fabrication of IPC-COF membranes. IPC-COF membranes with crystalline, rigid ion nanochannels exhibit a weakly humidity-dependent conductivity over a wide range of humidity (30–98%), 1–2 orders of magnitude higher than that of benchmark PEMs, and a prominent fuel cell performance of 0.93 W cm−2 at 35% RH and 80 °C arising from superior water retention and Grotthuss mechanism-dominated proton conduction.