Covalent organic framework (COF) is an emergent class of ordered porous materials with high stability. The fabrication of thin and continuous COF membrane for small molecule separation remains challenging due to the relatively large pore size of COF materials and weak COF-substrate interfacial interaction. Herein, a two-dimensional COF layer was spin-coated on a porous substrate followed by constructing a bio-inspired calcium alginate (Alg-Ca) layer to obtain a dual-layer membrane with a thickness less than 100 nm. The Alg-Ca layer afforded a superhydrophilic surface to capture water molecules, and the porous COF layer rendered selective water channels. The dual-layer membrane synergistically strenthened the solution-diffusion mechanism through the manipulation of the membrane structure and transport process. The synergy of two layers endowed the membrane with superior water-selective performance with permeation flux of 3614 g/(m(2)h) and water content in permeate of 99.7 wt% for n-butanol dehydration. The fabrication of dual-layer membrane in this study may offer a new strategy for highly efficient separation of liquid small molecule mixtures.