A disclosed method of processing a substrate includes (a) providing a substrate in a chamber of a plasma processing apparatus. The substrate has a patterned organic mask. The method further includes (b) generating plasma from a processing gas in the chamber in a state where the substrate is accommodated in the chamber. The method further includes (c) periodically applying a pulsed negative direct-current voltage to an upper electrode of the plasma processing apparatus, during execution of the generating plasma (that is, the above (b)). In the applying a pulsed negative direct-current voltage, ions from the plasma are supplied to the upper electrode, so that a silicon-containing material which is released from the upper electrode is deposited on the substrate.