A thermal power unit-flywheel energy storage cooperative frequency regulation control method and system is provided, which belongs to the technical field of a power grid. First, a real-time output increment of a thermal power unit is predicted, then a real-time frequency regulation power instruction of a flywheel energy storage system is determined based on the predicted real-time output increment of the thermal power unit, and finally the frequency regulation power instruction of the thermal power unit is determined by a difference adjustment coefficient of a governor and a grid frequency deviation. The thermal power unit and flywheel energy storage system is cooperatively controlled by frequency regulation based on the real-time output increment predicted value of the unit, which realizes self-adaptive adjustment of output of the flywheel energy storage system under dynamic working conditions, and improves the grid frequency stability and operation safety of the thermal power unit.