Mixed-matrix membranes (MMMs), consisting of nanoparticles and a polymeric matrix, have been proven high-efficiency separation media for gas separations. The interface engineering between the particles and polymeric matrixes is the key-point for MMMs to display an excellent separation performance. Herein, an amine modified ZIF-90 (ZIF-90-NH2) is dispersed in 6FDA-Durene to prepare MMMs, the modified amino groups can form the hydrogen bonding with 6FDA-Durene to enhance the compatibility of ZIF-90-NH2 and 6FDA-Durene. A 45 wt% ZIF-90-NH2/6FDA-Durene MMM demonstrated a high separation performance, surpassing the 2008 Robeson permeability-selectivity upper bounds. This satisfactory gas separation performance can be due to the intimate interactions between the 6FDA-Durene polymer and ZIF-90-NH2 nanoparticles via abundant hydrogen bonding. Furthermore, the covalent linkage of ZIF-90-NH2 with 6FDA-Durene can be driven by the tris(2-aminoethyl) amine (TAEA) vapor thermal modification method to realize the ring opening reaction, which further enhances the particles-polymer connection in the ZIF-90-NH2/6FDA-Durene-TAEA MMMs. Results show that the 45 wt% ZIF-90-NH2/6FDA-Durene-TAEA MMM exhibits a remarkably enhanced H2 permeability of 487.0 Barrer with a H2/CO2 selectivity of 35.8, which is 6.8 times higher than that of ZIF-90/6FDA-Durene-TAEA MMM. This strategy offers new prospects for membrane materials and opens a new way for the precise interface engineering of MMMs, and the resulting high performance for energy-efficient gas separations.