A power supply system of a plasma processing apparatus includes a radio frequency (RF) power supply, a bias power supply, and power supply controller circuitry. The RF power supply generates RF power for plasma generation. The bias power supply supplies an electric bias to a substrate support. The power supply controller circuitry periodically modulates a power level of the RF power in repetitions of a modulation cycle including at least two sub-periods. The power supply controller circuitry is configured to adjust a frequency of the RF power for an k-th phase period included in a feedback period continuing from a start time of each of the at least two sub-periods within the modulation cycle, based on a change in the frequency of the RF power and a change in a degree of reflection of the RF power in the k-th phase period in preceding repetitions of the modulation cycle.