Covalent triazine frameworks (CTFs) hosting arrays of highly ordered sub-2-nm pores are expected to exhibit unusual nanofluidic behaviors, which may enable important applications such as desalination. Herein, nonequilibrium molecular dynamics simulations are applied to investigate transport of water and ions inside two typical CTFs-CTF-1, and CTF-2-having intrinsic pores of 1.2 and 1.5 nm, respectively. Their monolayers exhibit extremely high water permeance but weak ion rejection. CTF multilayers are then investigated. Transport resistances composed of interior and interfacial contribution are correlated with stacking numbers of CTF monolayers to develop equations of predicting water permeance. It is revealed that both the stacking fashion and the number of CTF monolayers forming multilayers significantly influence permeation and ion rejection. Staggered multilayers exhibit much higher ion rejection than eclipsed ones. Staggered CTF-2 multilayers completely reject ions because the interlayer paths between two adjacent staggered monolayers allow only water molecules to pass through. Importantly, it is predicted from the equations that few-layered staggered CTF-2 multilayers, which can be relatively easily produced by experimental methods, exhibit 100% NaCl rejection and up to 100 times higher permeance than commercial reverse osmosis membranes, implying their great potential as building blocks to prepare next-generation desalination membranes.