A substrate processing method uses a substrate processing apparatus including a chamber for accommodating a substrate, a lower electrode to mount the substrate, a first RF power applying unit for applying an RF power for plasma generation into the chamber, and a second RF power applying unit for applying an RF power for bias to the lower electrode. The RF power for plasma generation is controlled to be intermittently changed by changing an output of the first RF power applying unit at a predetermined timing. If no plasma state or an afterglow state exists in the chamber by a control of the first RF power applying unit, an output of the second RF power applying unit is controlled to be in an OFF state or decreased below an output of the second RF power applying unit when the output of the first RF power applying unit is a set output.