The invention discloses a brake feedback device control system and method for counter current resistance of a power supply system. The control system comprises a counter current resistance monitoring device which is arranged at the connecting portion of a distribution transformer and a medium voltage looped network of the power supply system and at an outlet of the distribution transformer and is used for detecting current direction, and the counter current resistance monitoring device is in communication connection with an SCADA monitoring system which is used for being in communication connection with brake feedback current transformers. An existing system structure is used, counter current resistance monitoring devices are arranged at counter current resistance monitoring points, the current directions of distribution transformer sides at the monitoring points are monitored in real time, when counter currents are detected, counter current signals are issued to underground brake feedback devices through the SCADA monitoring system, and feedback output power on the medium voltage looped network is controlled to be lowered until the counter current signals disappear. The method is simple and easy to implement, intelligent control is achieved according to the practical situation, power supply system counter currents are avoided, and influence on safe reliable operation of a high-voltage power grid is avoided.