Provided is a substrate processing apparatus. The substrate processing apparatus includes a process chamber, a gas supply system, a gas discharge system, an RF (radio frequency) unit, an electrode, and a control device. The control device controls the gas supply system, the gas discharge system, and the RF unit. While the control device controls the RF unit to apply predetermined RF power to the electrode for generating plasma, the control device controls the gas supply system to supply a process gas to the process chamber alternately at a first flowrate and at a second flowrate greater than the first flowrate.