Separation of hydrogen from carbon dioxide for sustainable H2 production and CO2 capture still faces great challenges due to the smaller size of H2 and higher condensability of CO2. Herein, a high-performance benzimidazole-linked polymer (BILP) membrane for hydrogen separation was directly prepared on α-Al2O3 substrate through a facile interfacial polymerization approach at room temperature. The separation performance of the BILP membrane were regulated by controlling the reaction time and the microstructure was systematically characterized. Molecular simulations were performed to deep understand the separation mechanism in the BILP membrane. The best performance membrane displays an extraordinary mixed gas selectivity of 40 for H2/CO2 together with outstanding H2 permeance of 250 gas permeation units (GPU) at 473 K, far exceeding the Robeson’s upper bound. Besides, the membrane can withstand high temperature and pressure, and also shows good H2/N2 and H2/CH4 selectivity. The excellent separation performance, coupled with high temperature and pressure resistance and easy preparation, render BILP membranes great potential for economic H2 purification, H2 recovery, and natural gas treatment.