A surface modifying method of modifying a bonding surface of a substrate to be bonded to another substrate by plasma of a processing gas includes an adjusting process and a modifying process. In the adjusting process, an amount of moisture in a processing vessel is adjusted by supplying a humidified gas into the processing vessel allowed to accommodate the substrate therein. In the modifying process, the bonding surface of the substrate is modified by forming the plasma of the processing gas in the processing vessel in a state that the amount of moisture in the processing vessel is adjusted.