The invention discloses an intelligent control system of draining pumps in a transformer substation water collecting well. The intelligent control system comprises a plurality of draining pumps arranged in the water collecting well, a water level sensor, a current operation detecting device, a water pump control electrical cabinet, a water pump intelligent controller, an RCU intelligent terminal,a master station centralized control processing device and a transformer substation comprehensive monitoring center, wherein the draining pumps are connected with the water pump control electrical cabinet; each of the water level sensor, the current operation detecting device and the water pump control electrical cabinet is connected with the water pump intelligent controller; and the water pump intelligent controller, the RCU intelligent terminal, the master station centralized control processing device and the transformer substation comprehensive monitoring center are sequentially connected.The intelligent control system can avoid the phenomenon that the water pump refuses to start or is frequently started by mistake due to malfunction of a floating ball, the water level monitoring means is more stable and reliable, remote visual management of the water pump control can be realized, the reported data can be verified, and operation is visualized; and the current operation detecting device monitors the power supply current information of the water pump, can judge the operating(start-stop) state of the water pump and timely finds the failure state, so that precise maintaining datais provided for a maintaining staff, the source is saved, and the effect is enhanced.