Abstract: The present application provides a method and a device for synchronizing a high-speed quantum key generation system, wherein the method comprises: a sender aligns first light pulse of signal light with that of synchronization light, and controls the signal light not to emit light during N consecutive periods within each period Tt of the synchronization light; a receiver performs time measurement on received signal light pulse, the signal light emits light at the remaining corresponding positions except the N consecutive non-emitting positions in each period Tt, the emitting positions can join the statistical process of T1i and T2i, the statistical time is reduced by several orders of magnitude relative to the existing method of only sending single signal light pulse, and the statistical process can be completed in a few hundred milliseconds or even shorter.