The invention provides a satellite-borne clock redundant system and method. The satellite-borne clock redundant system and method are used for providing a system clock for a spaceflight control system. According to the system and method, an external high-accuracy clock and two internal clocks sources of which are not the same serve as a main clock, a backup clock and a third-party clock respectively, the third-party clock can be adopted for arbitration only when the main clock and the backup clock are inconsistent, single-redundancy faults of the clock can be allowed, the tri-redundancy aim is achieved, implementation is simple, and cost is low. According to the satellite-borne clock redundant system and method, the clock redundancy function of a control system is achieved through the high-accuracy clock of an inertia unit and the two clocks in a flight control computer, the high-accuracy clock of the inertia unit is sufficiently used, influences of faults of the clock on running of the control system are avoided, the reliability and the safety of the control system can be improved, and the satellite-borne clock redundant system and method have the advantages of being low in implementation cost and facilitating engineering realization.