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In this paper an efficient time-domain technique based on Prony's method for the time-varying power system harmonics estimation is proposed. Though the high frequency resolution is the major advantage of Prony's method, the great computational burden with the high estimation order usually makes it only suitable for the off-line analysis. To achieve the fast harmonic measurement, a filter-bank structure is proposed to reduce the computational complexity. Finally, the measurement results are reported to verify the performance of the proposed technique.