Radio frequency (RF) electronics are developing toward high power, high integration, and high-power density, resulting in a continuous increase in heat flux. The traditional high-power RF package, which is usually composed of aluminum nitride (AlN) substrate, aluminum silicon housing shell, and aluminum alloy cold plate, exhibits poor heat dissipation ability and high thickness due to excessive interfaces and a long thermal conduction path. In this paper, aimed at improving heat dissipation ability and reducing the thickness of RF electronics, the microchannel was transferred from the cold plate to the AlN high-temperature co-fired ceramic (HTCC) substrate which plays the role of electrical connection, structural support, and liquid cooling cold plate. The embedded AlN microchannel cooler was firstly designed. Then, a prototype of the AlN substrate with 64 simulated chip arrays and microchannels was fabricated and the thermal performance was evaluated using an experimental setup. Finally, the thermal performances of the proposed and traditional cooler were compared using a CFD simulation. The results indicated that the proposed embedded cooling structure could enhance the heat-flux dissipation ability by 61% and reduce the packaging thickness by 40% compared with the traditional cooling structure.