Novel polymer composite materials, including unique nanoparticles, contribute to the progress of modern technologies. In this work, the endohedral fullerene C60 with incapsulated iron atom (endometallofullerene Fe@C60) is used for modification of P84 copolyimide. The impact of 0.1, 0.5, and 1 wt % endometallofullerene on the structure and physicochemical properties of polymer films is studied through scanning electron microscopy, thermogravimetric analysis, and thermomechanical tests. Transport properties are estimated through sorption and pervaporation techniques toward methanol and methyl acetate mixture. The inclusion of endometallofullerene into the copolyimide matrix improves membrane permeability and selectivity in the separation of methanol—methyl acetate mixtures. The maximal effect is achieved with a composite containing 0.5 wt % Fe@C60. The developed composites are effective for energy and resource saving purification of methyl acetate by pervaporation.