Mixed matrix materials (MMMs) comprising porous fillers in polymers can exhibit superior gas separation properties, yet their practical use has been limited by poor interfacial compatibility between the two components. Herein we report a bottom-up approach to synthesize the MMMs by dispersing a metal-organic polyhedron (MOP-3) in monomer solutions before rapid photopolymerization to form interpenetrating networks (IPNs), where the porous MOP-3 nanoparticles serve as molecular dopants. Specifically, MOP-3 with particle sizes of ≈5 nm was dispersed in and infiltrated by either a macromonomer of poly(ethylene glycol) diacrylate (PEGDA) or poly(1,3 dioxolane) acrylate (PDXLA). The introduction of the MOP-3 in the polyethers decreases their glass transition temperatures and even induces the crystallization of polyPDXLA at high loadings. Increasing the MOP loading increases CO2 permeability with a slight decrease in CO2/gas selectivity. For example, as the MOP content increases from 0 to 30 mass% in polyPDXLA, CO2 permeability increases from 190 Barrer to 580 Barrer, and CO2/N2 selectivity decreases from 70 to 62 at 35 °C. These IPNs-based MMMs exhibit separation properties above the Robeson's upper bounds for CO2/N2 and CO2/H2 separation. As the MOPs are soluble in solvents, this approach can be easily integrated into industrial membrane fabrication processes to produce MMMs-based composite membranes in large-scale.