The invention provides a cooling system based on the multi-layer structure of a graphene composite/silicon nitride/silicon chip, and an establishing method of the cooling system, and belongs to the cooling technology of microelectronic devices. A cooling framework comprises a silicon-based heating device, a Si3N4 insulating layer, a graphene composite heat sink and a base plate. The dense Si3N4 insulating layer is deposited on the back face of a silicon wafer through a chemical gas-phase depositing method, a graphene composite and the Si3N4 insulating layer are connected through a chemical bond, and finally the silicon wafer with the cooling framework and the base plate are connected and packaged into a device. The silicon-based heating device, a thermal interface material and the heat sink are connected through chemical bonds, and therefore the distances of device layers are greatly reduced, thermal resistance caused by interlayer micro gaps is avoided, phonon thermal conductance is promoted, the cooling capacity of the whole cooling system is improved, and the chip can work at a severe high temperature. After package, the whole system is lighter and thinner and meets the development tendency of an up-to-date semiconductor device.