The invention relates to the field of water supply control, in particular to a water pump control system used for the low water period of power plant construction. The water pump control system comprises a main pump and a standby pump which are located at two water sources. The main pump and the standby pump are connected with a water tank of a living area through pipelines. A flow switch K2 is mounted at a main water inlet pipe in front of the water tank and controls starting and stopping of the water pumps according to the flow. A control circuit comprises a main switch CB, a main pump contactor KM1 and a standby pump contactor KM2, wherein the main pump contactor KM1 and the standby pump contactor KM2 are in parallel connection and are both connected with the flow switch K2. A normally-closed contact of the standby pump contactor KM2 is in series connection with the main pump contactor KM1. The two water pumps are arranged to operate respectively. When the flow of the main pump is reduced, the main pump stops operating, and meanwhile the standby pump is automatically started. When the flow of the standby pump is reduced, the main pump and the standby pump stop operation simultaneously. After water level of a water well recovers in a certain time, control circulation can be repeated till the water tank is injected to the standard water level, and overburning of the water pumps is avoided.