A substrate plasma processing apparatus includes a substrate holding electrode and a counter electrode which are arranged in a chamber, a high frequency generating device which applies a high frequency of 50 MHZ or higher to the substrate holding electrode, a DC negative pulse generating device which applies a DC negative pulse voltage in a manner of superimposing on the high frequency, and a controller controlling to cause intermittent application of the high frequency and cause intermittent application of the DC negative pulse voltage according to the timing of on or off of the high frequency.