Mixed matrix composite membranes (MMCMs) hold great potential to realize efficient CO2 removal from natural gas. However, the reduction of separation performance arising from the interfacial defects, significant plasticization and aging effect in the thin films severely limit their application. Herein, we fabricated a series of polyimide MMCMs with MOF-protruding structure wherein amino-functionalized ZIF-8 nanocrystals nearly penetrate the thin selective layer. Through engineering the interfacial interactions, e.g., covalent or hydrogen bondings, we successfully fabricated defect-free MMCMs with the thickness ranging from 140 to 280 nm. The stronger interfacial interactions eliminate the interfacial defects and restrict the mobility of polymer chains under high pressure. Accordingly, the MMCM displays a high CO2 permeance of 778 GPU and a CO2/CH4 selectivity of 34 with significantly improved resistance to plasticization and aging. Considering the superior performance, we anticipate our work could provide guidelines on designing advanced MMMs to tackle critical separations.