Mixed matrix membranes (MMMs) attract great attention due to their outstanding gas separation performance. The compatibility between the fillers and the polymer matrix is one of the key points for the preparation of high-performance MMMs. In this work, MMMs consisting of metal-organic frameworks (MOFs) of amine-modified Cu-BTC (NH₂-Cu-BTC; BTC = 1,3,5-benzenetricarboxylic acid) and submicrometer-sized amine-modified Cu-BTC (sub-NH₂-Cu-BTC) incorporated into a Pebax-1657 polymer were fabricated for the gas separation. The SEM image and Fourier transform infrared spectroscopy (FTIR) spectra showed an increase in the surface roughness of MOFs and the presence of amino groups on the surface of Cu-BTC after the amination modification, and a decrease in the size of MOFs crystals after the submicrometer-sized aminated modification. Gas adsorption analysis indicated that NH₂-Cu-BTC and sub-NH₂-Cu-BTC had a higher gas adsorption capacity for CO₂ compared to the unmodified Cu-BTC. The scanning electron microscopy (SEM) image showed that NH₂-Cu-BTC and sub-NH₂-Cu-BTC, especially sub-NH₂-Cu-BTC, had a better compatibility with a polyether-block-amide (Pebax) matrix in the MMMs. The gas separation performance indicated that the Pebax/sub-NH₂-Cu-BTC MMMs evidently improved the CO₂/N₂ and CO₂/CH₄ selectivity at the expense of a slight CO₂ permeability. The results reveal that modified MOF-filled MMMs possess great potential for applications in the CO₂ separation field.