Abstract The covalent organic frameworks (COFs) possessing high crystallinity and capability to capture low‐concentration CO 2 (400 ppm) from air are still underdeveloped. The challenge lies in simultaneously incorporating high‐density active sites for CO 2 insertion and maintaining the ordered structure. Herein, a structure engineering approach is developed to afford an ionic pair‐functionalized crystalline and stable fluorinated COF (F‐COF) skeleton. The ordered structure of the F‐COF is well maintained after the integration of abundant basic fluorinated alcoholate anions, as revealed by synchrotron X‐ray scattering experiments. The breakthrough test demonstrates its attractive performance in capturing (400 ppm) CO 2 from gas mixtures via O─C bond formation, as indicated by the in situ spectroscopy and operando nuclear magnetic resonance spectroscopy using 13 C‐labeled CO 2 sources. Both theoretical and experimental thermodynamic studies reveal the reaction enthalpy of ≈−40 kJ mol −1 between CO 2 and the COF scaffolds. This implies weaker interaction strength compared with state‐of‐the‐art amine‐derived sorbents, thus allowing complete CO 2 release with less energy input. The structure evolution study from synchrotron X‐ray scattering and small‐angle neutron scattering confirms the well‐maintained crystalline patterns after CO 2 insertion. The as‐developed proof‐of‐concept approach provides guidance on anchoring binding sites for direct air capture (DAC) of CO 2 in crystalline scaffolds.