The controlling nanofiller aggregation and strengthening interfacial interaction are of great scientific significance for mixed matrix membranes (MMMs). In this study, the polymer-embedded metal-organic framework (pMOF) microspheres (MSs) are designed by one-pot synthesis and employed as microfillers for improving separation performance of MMMs. Through adding polymer during solvothermal crystallization, the polymer chains are embedded into the MOF materials, and the morphologies of the MOFs are transformed from nanopaticles to polycrystalline MSs. Since the embedding of the identical polymer promotes the compatibility of polymeric matrixes and fillers, as well as the micrometer-sized porous MSs offer additionally superior and permanent transport pathways, the resulted MMMs display simultaneously enhanced selectivity and permeability for carbon capture. The CO2/CH4 selectivity and CO2 permeability of the pMOF MMMs are achieved at 1.3 and 2.2 times as those of the pure polymeric membranes, and 1.5 and 1.2 times as those of the MOF MMMs, respectively.