A novel vector estimation method for PMUs in power system is proposed, which is based on all-phase fast Fourier transform (apFFT). Due to apFFT’s excellent performance in suppressing spectral leakage and the property of ‘phase invariant’, this method can realize the accurate estimation of PMU phase angle, and then the time-shift phase difference spectrum correction is adopted to estimate the frequency and amplitude parameters. The calculation flow of this algorithm is proposed, and the hardware of new measuring device is designed based on ARM9 microprocessor. Simulation results show that the proposed method is close to unbiased estimation for noise-free case, and the algorithm in this paper can obtain 7dB signal-to-noise ratio gain compared with the conventional method.