Mixed matrix membranes (MMMs), combining the advantages of polymer membranes and porous materials, processing the potential to realize large-scale gas separation applications. However, the interfacial defects in MMMs greatly hindered gas separation performance improvement. Therefore, designing an MMM with high loading and good interfacial compatibility remains a critical issue in promoting the application of MMMs. Herein, during in-situ heating process, the melting of liquid ZIF-62 in PBI polymer can largely fill the interfacial defects in MMMs. The microporous transport channels of ZIF-62 glass in MMMs promoted the H2 diffusion and inhibited the CO2 and CH4 diffusion, thus enhancing the H2/CO2 and H2/CH4 separation of MMMs. For mixed gas testing, the 45 wt% ZIF-62 glass/PBI membrane had the maximum H2 permeability of 459 barrer, and its H2/CO2 and H2/CH4 selectivities were 23 and 57, higher than the gas separation upper bonds. In addition, ZIF-62 glass/PBI membrane exhibited stable separation performance under 1–5 bar pressure. Therefore, the rational combination of MOF glass and polymer matrix could provide promising potential for reducing the interfacial defects of high-loading MMMs, thus enhancing the gas separation performance.