In non-destructive granular material dielectric measurement, microwave cavity resonator technique which is dependent against varied size and shape of cavity is suitable. Since the transmitted microwave should equally cover around the shape, system design is needed to consider transmitted microwave equally covering all area of cavity. This paper proposes a system of microwave cylindrical cavity resonator using combination of circular and rectangular waveguides for granular material dielectric measurement. In the system, the waveguide transmitters which are circular and rectangular waveguides are set in the perpendicular position to propagate the microwave into the resonator. The microwave that is excited by these waveguides propagates to receiver port for subsequent analysis. The resonator dimension is designed for resonant at 2.45 GHz and TE111 mode which is the dominant mode of cylindrical resonator. The distribution of electric field from two combination waveguide transmitters cover to the cylindrical cavity resonator or all of the material inside the resonator can absorb the electromagnetic wave. Finally, the electromagnetic wave can propagate to the receiver port for additional analysis. The prototype has been constructed according to proposed concept, and the evaluation results are demonstrated by simulation.