The invention relates to a robust control system and a robust control method for an electric time synchronization system. The time synchronization system comprises at least two master clock devices and a slave clock device, wherein the master clock devices are interconnected via an optical fiber; the master clock devices are interconnected with the slave clock device via the optical fiber; the time synchronization system receives an external time source signal via the master clock devices, so that safety and reliability of time source selection of the master clock devices can be ensured by ensuring the safety and reliability of the external time source signal; each master clock device is composed of a clock receiving unit, a clock unit and an output unit connected in sequence; and the time synchronization system is provided with a reliability judging module on the clock receiving unit and the clock unit.According to the system and the method provided by the invention, beginning with signal sources of the time synchronization system, signal security of the input time source is judged by introducing the plurality of external time sources, interference of the external instable signal and malicious tampering of the input time source signal are completely eradicated, and thus the most reliable time source is selected to serve as the synchronization time source of the master clock devices, and reliability of the time source signal of the master clock devices is ensured.