Sulfonated covalent organic frameworks (SCOFs) facilitate rapid proton conduction through densely ordered sulfonic acid groups, however, the brittleness of COFs self-supporting membranes often makes potential difficulty in fuel cell assembly and limits their power density. Herein, a highly flexible SCOF proton exchange membrane is developed through in-situ growth of a continuous BD(SO3H)2-COF microphase within porous PTFE networks. The strong hydrogen bonding between PTFE and BD(SO3H)2-COF contributes to the defect-free morphology of the BD(SO3H)2/PTFE membrane. The reinforce of PTFE network makes the membrane extremely high flexibility, achieving an elongation at break of 124.4% even with a remarkably high SCOF mass proportion of 90 wt.% (BD(SO3H)2/PTFE-0.9). This allows the membrane to be folded repeatedly, even in dry state. The swelling ratio in water at 80 °C is effectively restricted to 8.6%, even with a high ion exchange capacity of 3.6 mmol g-1 and a water uptake of 68.2%. The densely ordered sulfonic acid groups in continuous BD(SO3H)2-COF microphase contribute to a high proton conductivity up to 249.2 mSꞏcm-1 at 80°C, approximately 1.5 folds that of Nafion 212. As a result, the BD(SO3H)2/PTFE-0.9 membrane achieves a fuel cell power density of 1195.3 mWꞏcm-2 at 80°C, along with a high open circuit voltage of 1.01 V, surpassing the-state-of-the-art COF-based proton exchange membranes. This work provides a novel strategy to fabricate COFs into flexible and size scalable membranes, enhancing the performance of fuel cells.