Developing new materials for the fabrication of proton exchange membranes (PEMs) for fuel cells is of great significance. Herein, a series of highly crystalline, porous, and stable new covalent organic frameworks (COFs) have been developed by a stepwise synthesis strategy. The synthesized COFs exhibit high hydrophilicity and excellent stability in strong acid or base (e.g., 12 m NaOH or HCl) and boiling water. These features make them ideal platforms for proton conduction applications. Upon loading with H3PO4, the COFs (H3PO4@COFs) realize an ultrahigh proton conductivity of 1.13×10−1 S cm−1, the highest among all COF materials, and maintain high proton conductivity across a wide relative humidity (40–100 %) and temperature range (20–80 °C). Furthermore, membrane electrode assemblies were fabricated using H3PO4@COFs as the solid electrolyte membrane for proton exchange resulting in a maximum power density of 81 mW cm−2 and a maximum current density of 456 mA cm−2, which exceeds all previously reported COF materials.