The separation performance of mixed matrix membranes (MMMs) is greatly impacted by both the inherent structure of porous fillers and the interfacial compatibility between the filler and matrix. Here, ultra-small Zr-MOFs (UiO-66-mod and NH2-UiO-66-mod) with more defect sites were synthesized through a simple sodium formate modulation strategy. Then, these modulated Zr-MOFs were used as porous fillers in combination with polyetherimide (PEI) to construct a high-quality mixed matrix membrane for efficient CO2 separation. The modulated Zr-MOF not only exposed more defect sites, which significantly enhanced the CO2 adsorption capacity but also exhibited high dispersion in the PEI matrix due to strong interfacial forces, avoiding non-selective voids. The 10-UiO-66-mod-PEI and 10-NH2-UiO-66-mod-PEI membranes developed here showed admirable CO2/CH4 separation performance (CO2 permeability of around 400 and 440 Barrer, CO2/CH4 selectivity of ∼33 and ∼47, respectively) much higher than that of non-modulated UiO-66-PEI membranes, surpassing the 2008 upper bound of MMMs. This work demonstrated that the proposed UiO-66-mod-PEI and NH2-UiO-66-mod-PEI MMMs could be potential candidates for an efficient CO2 capture process.