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Covalent linkages are the key component of covalent organic frameworks (COFs). The development of stable and functional linkages is essential to expand the COFs family and broaden their application prospects. In this work, we report the synthesis of crystalline and chemical stable 4-carboxyl-quinoline linked COFs (QL-COFs) via Doebner reactions in both one-pot (OP) and post-synthetic modification (PSM) methods. Both methods can be universally applied to most of the reported imine COFs family via bottom-up construction or linkage conversion. Owing to the contractive pore size, more hydrophilic structure and better chemical stability than the conventional imine COFs endowed by 4-carboxyl-quinoline linkage, QL-COFs are supposed to possess a wider application range. We further demonstrate the nanofiltration membrane (NFM) based on QL-COF exhibited a desirable separation capacity with high rejection for small dye molecules (> 90%), high water permeance (850 L m−2 h−1 MPa−1) and tolerance of extreme conditions (1 M HCl/NaOH), which were benefitted from the enhanced properties of QL-COFs. Additionally, efficient ion sieving properties were also achieved by QL-COF membrane. We anticipate that this work opens up a way for the construction of robust and functional COFs materials for practical applications.