A substrate processing apparatus includes a processing chamber; a susceptor provided in the processing chamber, wherein the susceptor is configured to support a substrate; a first plasma generator disposed on one side of the processing chamber; and a second plasma generator disposed on another side of the processing chamber, wherein the second plasma generator is configured to generate plasma by simultaneously supplying a sinusoidal wave signal and a non-sinusoidal wave signal to the susceptor. By using a substrate processing apparatus, a signal source device, and a method of processing a material layer according to the inventive concept, a smooth etched surface may be obtained for a crystalline material layer without a risk of device damage by RDC.