Covalent organic frameworks (COFs) have received considerable attention in molecular separation due to their tunable structures. However, how to determine the optimal number of layers for a COF is lack of theoretical guidance while considering tradeoff effect between water flux and rejection. Herein, the transport behavior of water and ions as a function of layer number was investigated for multilayered TpPa-(OMe)2 COFs with nonequilibrium molecular dynamics simulations. With an increase in the layer number from 2 to 6, the ion rejection was enhanced from 50% to nearly 90%. We attributed this phenomenon to the dehydration of ions entering the pore opening and a stronger interaction of Mg2+ than water with the internal groups of the COFs. Our data suggests that an optimal number of TpPa-(OMe)2 layers is 6. Under these conditions the COFs exhibited 90% MgCl2 rejection, whereas water permeance is 2 orders of magnitude higher than commercial nanofiltration membranes.