The invention discloses a backup clock for an electronic current transformer and an operation method thereof. The backup clock for an electronic current transformer comprises a digital phase detector, a digital loop filter and a numerically-controlled oscillator, wherein the digital phase detector comprises a D trigger and a locking circuit; the input end of the D trigger receives input clock signals, and the other input end is connected with the numerically-controlled oscillator; the locking circuit is connected with the numerically-controlled oscillator; the digital loop filter comprises a reversible counter and a comparator, the reversible counter is respectively connected with the D trigger and the numerically-controlled oscillator, and the reversible counter is connected with the comparator; and the numerically-controlled oscillator comprises a phase controller, a frequency divider and a crystal oscillator, the phase controller is connected with the comparator, the phase controller is connected with a signal clock, the phase controller is connected with the frequency divider, and the frequency divider is connected with the crystal oscillator. The local clock and the input signals are synchronous, the plus/minus pulse-type numerically-controlled oscillator is adopted, pulses are added and subtracted in precise and rough adjustment modes, and the synchronous speed of the backup clock is greatly improved.