Photocatalytic conversion of solar energy to generate green hydrogen is considered to be one of the most promising methods in response to the energy problem. Recently, covalent organic frameworks (COFs) have emerged as a potential new class of materials in photocatalytic hydrogen production. Herein, a planar and strong donor–acceptor (D–A) COF was constructed by simply introducing strongly electronegative F atoms. By experiments and theoretical calculations, the key role of F was verified in charge separation and transfer. On the one hand, it can form intramolecular hydrogen bonds, reducing the torsion angle caused by steric hindrance and maintaining AA′ positive stacking mode, which promotes charge transfer in the axial direction. On the other hand, the enhanced electron-withdrawing effect could increase the intrinsic separation driving force of charge separation and enhance π–π interactions, thus prolonging the lifetime of carriers between COF layers and reducing charge recombination. As a result, COF-F performed the highest photocatalysis hydrogen evolution of 10.58 mmol g–1 h–1 (52.9 μmol h–1) than COF-H and COF-Cl. Thus, this work provides novel insight into designing COF photocatalysts with enhanced charge separation and transfer efficiency by molecular structure engineering.