The invention discloses an unsteady flow control system for a hydropower station downstream model test. The unsteady flow control system compiles a flow change process of unsteady flow into a data file corresponding to time flow, wherein a control terminal is used for continuously sending the corresponding flow to a frequency conversion module according to the time in the data file; the frequencyconversion module is used for converting the flow into water pump motor frequency and sending the water pump motor frequency to a frequency converter; and the water pump motor frequency is controlledthrough the frequency converter, so that a water pump conveys water from an underground reservoir to a model forebay according to the flow change process of the unsteady flow compiled in the data file; an electric valve is arranged between the model forebay and a model downstream river channel, and the control terminal controls the opening degree of the electric valve according to the real-time flow fed back by an electromagnetic flowmeter and the real-time water level of the model forebay, so that the unsteady flow is controlled again. The unsteady flow control system is high in response speed and control precision, and the unsteady flow process of flow discharge of a power station can be accurately simulated and completely automatically controlled.