Amphiphilic poly(dimethylsiloxane-ethylene-propylene oxide)-polyisocyanurate cross-linked block copolymers based on triblock copolymers of propylene and ethylene oxides with terminal potassium-alcoholate groups (PPEG), octamethylcyclotetrasiloxane (D4) and 2,4-toluene diisocyanate (TDI) were synthesized and investigated. In the first stage of the polymerization process, a multiblock copolymer (MBC) was previously synthesized by polyaddition of D4 to PPEG. The usage of the amphiphilic branched silica derivatives associated with oligomeric medium (ASiP) leads to the structuring of block copolymers via the transetherification reaction of the terminal silanol groups of MBC with ASiP. The molar ratio of PPEG, D4, and TDI, where the polymer chains are packed in the “core-shell” supramolecular structure with microphase separation of the polyoxyethylene, polyoxypropylene and polydimethylsiloxane segments as the shell, was established. Polyisocyanurates build the “core” of the described macromolecular structure. The obtained polymers were studied as membrane materials for the separation of gas mixtures CO2/CH4 and CO2/N2. It was found that obtained polymers are promising as highly selective and productive membrane materials for the separation of gas mixtures containing CO2, CH4 and N2.