Developing novel materials for membrane separation is extremely crucial. Benzimidazole-linked polymers (BILPs) show great potential for H2 purification due to their high thermal and chemical stability, while only a few BILPs have been used for membrane-based gas separation. In this work, the BILP-5 composite membranes were prepared via a facile interfacial polymerization. Dense and smooth BILP-5 composite membranes were prepared on α-Al2O3 support and characterized by scanning electron microscope (SEM) and atomic force microscope (AFM). The effects of interfacial polymerization reaction duration, temperature, and pressure on the gas separation performance of BILP-5 membranes were systematically investigated. The resultant BILP-5 membrane shows good stability and a high H2/CO2 selectivity of 16 with a H2 permeance of 362 GPU under mixed gas test at room temperature, which exceeds the 2008 upper bound. Furthermore, the H2/CO2 separation mechanism of BILP-5 membranes was investigated through molecular dynamics simulations. Coupled with the merits of simple preparation, good stability, and excellent gas separation performance, BILP-5 is expected to be one of the most promising membrane materials for H2/CO2 separation.