Mixed matrix membrane (MMM) is one of the most promising candidates for exceeding the gas separation upper bound, while fillers can largely determine their ultimate performance. The molecular imprinting technique was first employed to prepare a layer containing rich CO2 adsorption sites on the UiO-66-NH2 surface for fabricating highly CO2-permeable PIM-1-based MMMs with higher selectivity. Transmission electron microscopy (TEM) and element mapping confirmed the successful formation of the core-shell structure for the imprinted metal-organic frameworks (MOFs). The MMMs prepared with imprinted MOFs present enhanced CO2 permeability and CO2/N2 selectivity, higher compatibility between polymers and fillers, and better mechanical strength compared to the MMMs with the pristine UiO-66-NH2. The MMMs formed with 5 wt% imprinted MOFs showed superior CO2/N2 separation performance beyond the 2019 upper bound with an ultrahigh CO2 permeability of 13,000 barrer (increased twice compared to pristine PIM-1 membrane). Moreover, with a filler content of 13 wt%, the obtained membrane maintains good mechanical properties, which indicates the benefit of the imprinted layer for the improvement of the filler loading inside a PIM-1 matrix. The membranes showed decreased CO2 permeability and CO2/N2 selectivity under the wet conditions, but stable performances over 46 hours of dynamic testing. The results indicate the presented approach for filler modification via molecular imprinting is a promising strategy for the enhancement of the MMM separation performance.