A periodically patterned and magnetized medium for controlling spin waves is proposed in a magnonic device and presents a clear advantage compared with other metamaterials because of the tunability in reconfiguring its pattern during operation. We study the spin-wave propagation numerically by controlling the arrangement of two magnetic Skyrmion arrays instead of patterned structures. The adjustment the position of each of the Skyrmion arrays could result in distinct spin-wave propagation or refraction depending on the location of the Skyrmions in each array. Control of the arrangement of two Skyrmion arrays can be made by an asymmetric magnetic field generated by a symmetric electrode with different current directions. This simple method of spin-wave manipulation can be applied to the development of magnonic devices consisting of Skyrmions as the building blocks of the magnonic crystals.