Covalent organic frameworks (COFs) have gained increasing interest as promising building blocks for desalination membranes due to their inherent porosity. Efforts have been made to prepare COF membranes and explore their transport mechanisms, however the effect of tautomerization has not been reported. Using non-equilibrium molecular dynamics, we discover here that a mere 0.5-Å atomic displacement between two tautomers of an imine-based COF (TpHZ) can surprisingly lead to dramatic changes in the desalination behavior of their multilayers. The tautomeric transformation (from TpHZ-NH to TpHZ-OH) improves the water permeability by about 1.6–3 times. The interior resistance rather than the entrance resistance is found to dominate the water transport. The weaker adhesion and the smoother channel path of TpHZ-OH result in a much lower interior resistance. Furthermore, NaCl rejection increases from ∼ 89 % to 100 % due to the stronger sieving effect resulting from the reduced compensatory effect of TpHZ-OH for ion hydrations.