Covalent organic frameworks (COFs) with long-range ordered, rigid, and tailor-made nanochannels hold great promise for energy-related applications. Here, we fabricate COF membranes with one-dimensional charged nanochannels using ionic COF nanosheets decorated with sulfonic acid groups. The free-standing and robust COF membrane exhibits enhanced proton conductivity and suppressed methanol permeability compared to the benchmark Nafion membrane. More interestingly, the methanol permeability of the COF membrane remains almost constant in a wide range of methanol concentrations (5.35 × 10−7 cm2 s−1 for the 2 M methanol/water mixture and 5.44 × 10−7 cm2 s−1 for the neat methanol). All-atomistic dynamics simulations indicate that the diffusio-osmotic effect arising from the charged nanochannels can account for the low and nearly constant methanol permeability of the COF membranes. These findings suggest that the ionic COF membranes can find potential applications in direct methanol fuel cell with high methanol concentrations, and meanwhile shed light on the mass transport mechanism in the charged, rigid and ordered nanochannels.