A control system of a variable speed pumped storage hydropower system comprising: a secondary excitation device configured to apply a current to a secondary winding of a generator-motor; a flow rate adjusting valve control unit configured to control an opening of a flow rate adjusting valve that adjusts a flow rate of a pump-turbine connected with the generator-motor; an optimization processing unit configured to generate a generator-motor output command value based on a demanded generator-motor output, and to calculate and output a flow rate adjusting valve opening demand value and a first command value from a head value and the generator-motor output command value, the first command value including a slip command value, a rotational speed command value, an angular velocity command value, or a secondary frequency command value; and a speed control unit configured to generate a secondary current active power component command value of the secondary excitation device based on the first command value; wherein the control system is characterized by further comprising: an output compensation unit configured to calculate a compensation value of the secondary current active power component command value by using a power system frequency deviation; a mechanical output compensation unit configured to input an output of the output compensation unit, and to calculate at least either a compensation value of the opening of the flow rate adjusting valve or a compensation value of the generator-motor output; and an output control unit configured to generate a flow rate adjusting valve opening command value based on the generator-motor output command value, the flow rate adjusting valve opening demand value, the compensation value calculated by the mechanical output compensation unit, and an output detection value of the generator-motor, and to output the flow rate adjusting valve opening command value to the flow rate adjusting valve control unit. a secondary excitation device configured to apply a current to a secondary winding of a generator-motor; a flow rate adjusting valve control unit configured to control an opening of a flow rate adjusting valve that adjusts a flow rate of a pump-turbine connected with the generator-motor; an optimization processing unit configured to generate a generator-motor output command value based on a demanded generator-motor output, and to calculate and output a flow rate adjusting valve opening demand value and a first command value from a head value and the generator-motor output command value, the first command value including a slip command value, a rotational speed command value, an angular velocity command value, or a secondary frequency command value; and a speed control unit configured to generate a secondary current active power component command value of the secondary excitation device based on the first command value; wherein the control system is characterized by further comprising: an output compensation unit configured to calculate a compensation value of the secondary current active power component command value by using a power system frequency deviation; a mechanical output compensation unit configured to input an output of the output compensation unit, and to calculate at least either a compensation value of the opening of the flow rate adjusting valve or a compensation value of the generator-motor output; and an output control unit configured to generate a flow rate adjusting valve opening command value based on the generator-motor output command value, the flow rate adjusting valve opening demand value, the compensation value calculated by the mechanical output compensation unit, and an output detection value of the generator-motor, and to output the flow rate adjusting valve opening command value to the flow rate adjusting valve control unit. an output compensation unit configured to calculate a compensation value of the secondary current active power component command value by using a power system frequency deviation; a mechanical output compensation unit configured to input an output of the output compensation unit, and to calculate at least either a compensation value of the opening of the flow rate adjusting valve or a compensation value of the generator-motor output; and an output control unit configured to generate a flow rate adjusting valve opening command value based on the generator-motor output command value, the flow rate adjusting valve opening demand value, the compensation value calculated by the mechanical output compensation unit, and an output detection value of the generator-motor, and to output the flow rate adjusting valve opening command value to the flow rate adjusting valve control unit.