This study incorporated multiwalled carbon nanotubes (MWCNTs) containing different functional groups (MWCNT-NH2, MWCNT-OH, and MWCNT-COOH) into a 6FDA-based copolyimide with a crown ether structure (6FDA-HFBAPP/DAB18C6). The incorporation of functionalized MWCNTs improved the gas permeability of polyimide. MMMs with MWCNT-OH and MWCNT-NH2 showed significant increases in gas permeability with higher filler content while maintaining high gas selectivity. Gas permeability enhancement in MMMs occurred via two mechanisms: (1) intrinsic MWCNT tunnels acting as fast gas channels and (2) increased free volume between the polymer and MWCNTs, providing more diffusion pathways. Notably, PI/MWCNT-NH2 with 1 wt % loading maintained comparable selectivity (65.25 for the CO2/N2 gas mixture and 100.82 for the CO2/CH4 gas mixture) while increasing CO2 permeability by 36–40% (from 95.6 to 134.3 Barrer for the CO2/N2 gas mixture and from 92.8 to 125.9 Barrer for the CO2/CH4 gas mixture), highlighting its potential for CO2 separation in PI-based MMMs.