Branched polyethyleneimine (PEI) functionalized UiO‐66 were synthesized and used as fillers to fabricated mixed‐matrix membranes (MMMs) for CO2/CH4 separation. The purpose of introducing amino‐functional groups in the filler is to improve the interfacial compatibility of the filler with the polymer through the formation of hydrogen bonds with the carbonyl group of 6FDA‐ODA. Additionally, the amino group can facilitate CO2 transport through a reversible reaction, enhancing the CO2/CH4 separation properties of MMM. The chemical structure and morphology of fillers and membranes were characterized by employing X‐ray photoelectron spectroscopy (XPS), Fourier transform infrared spectrometer (FTIR), X‐ray diffraction (XRD), thermogravimetric (TGA), Derivative thermogravimetry (DTG) and scanning electron microscope (SEM). Furthermore, the effects of filler loading and feed pressure on CO2 permeability and CO2/CH4 selectivity have been investigated. MMMs present higher gas separation performance than pure 6FDA‐ODA due to the presence of amino groups and the improvement of interface morphology. In particular, the MMM with 15 wt% loading of UiO‐66‐PEI shows optimum CO2 permeability of 28.23 Barrer and CO2/CH4 selectivity of 56.49. Therefore, post‐synthetic modification of UiO‐66 particle with PEI is a promising alternative to improved membrane performance.