Gas separation efficiency of covalent organic framework (COF) membrane can be greatly elevated through precise functionalization. A pair-functionalized COF membrane of 1,3,5-triformylphloroglucinol (TP) and isoquinoline-5,8-diamine (IQD) monomers in two and three nodes is designed and synthesized. TP-IQD is crystallized in a two-dimensional structure with a pore size of 6.5 Å and a surface area of 289 m2 g-1 . This COF possesses N-O paired groups which cooperatively interact with C2 H2 instead of C2 H4 . TP-IQD nanosheets of ≈10 μm in width and ≈4 nm in thickness are prepared by mechanical exfoliation; they are further processed with 6FDA-ODA polymer into a hybrid membrane. High porosity and functionality pair of TP-IQD offer the membrane with significantly increased C2 H2 permeability and C2 H2 /C2 H4 selectivity which are 160 % and 430 % higher of pure 6FDA-ODA. The boosted performance demonstrates high efficiency of the pair-functionality strategy for the synthesis of separation-led COFs.