The disclosed plasma processing apparatus is provided with a chamber, a substrate support, and a power source system. The substrate support has an electrode and configured to support a substrate in the chamber. The power source system is electrically connected to the electrode and configured to apply a bias voltage to the electrode to draw ions from a plasma in the chamber into the substrate on the substrate support. The power source system is configured to output a first pulse to the electrode in a first period and output a second pulse to the electrode in a second period after the first period, as the bias voltage. Each of the first pulse and the second pulse is a pulse of a voltage. A voltage level of the first pulse is different from a voltage level of the second pulse.