MOF mixed-matrix membranes (MMMs) are regarded as promising candidates for energy-efficient natural gas purification. This work reports the fabrication of high-performance 6FDA-polyimide MMMs, based on the incorporation of zeolite-like MOF (ZMOF) as fillers, and their associated permeation studies for CO2/CH4 separation. To eliminate micron-sized crystals, a facile repeating sedimentation approach was used to harvest nanocrystals from the as-synthesized bulk ZMOF crystalline powder material. This enables the deployment of ZMOF nanocrystals with relatively uniform dimension and morphology in the polymer matrix. Typical 6FDA-polyimides encompassing distinct diamine moieties (6FDA-DAM, 6FDA-DETDA-DABA or PDMC) were explored as polymer matrices to disclose the transport property matching the hosted ZMOF filler. Mixed-gas permeation measurements revealed that the incorporation of the ZMOF filler affords a concurrent enhancement of the CO2 permeability and the CO2/CH4 selectivity for the three tested 6FDA-polyimides. Particularly, the highly permeable 6FDA-DAM showed a considerably enhanced performance for CO2/CH4 that transcends the 2008 Robeson upper-bound. Detailed analysis of the sorption data and diffusion coefficients suggest that the enhanced transport property in the ZMOF-based MMM is plausibly attributed to the combination of the higher CO2 sorption capacity and selectivity, and favorable gas diffusivity via the CO2-philic framework of ZMOF in moderately confined pores.