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When the Three-phase power signal containing multiple harmonics signal, there is a clear error that FFT algorithm is used directly to measure the phase. Even with the various correction methods such as ratio method, center of energy gravity method etc., precision is severely constrained by harmonic signal. To solve these problems, a modified FFT algorithm, which is all-phase FFT, is used to measure the phase difference of three-phase power. The algorithm makes phase measurement accuracy significantly improve. More importantly, this method is almost immune to harmonic noise, and easily implements in hardware to meet real-time measurement of power system requirements.