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Frequency is one of the most significant indicators of power system, which needs accurate estimation to provide a reliable basis for monitoring, control, and protection. Owning to the efficiency, DFT is widely used in the frequency measurement of power systems. However, the inherent defects, that is, the spectral leakage and picket fence effect, decrease the accuracy of DFT. One of the variants, named the windowed phase difference method (WPD), addresses the problem using the phase variation of two windowed sequences in the frequency domain and achieves accurate frequency estimation. Suffering from the ignored negative component and contamination of noise, there are still undesired errors in WPD-based frequency estimation. To reduce the influence of the undesired errors, this paper first analyzes the systematic error of WPD introduced by spectrum leakage and proposes an improved WPD (IWPD) through systematic error compensation to achieve more accurate frequency estimations. Then, the windowing effect on IWPD-based frequency estimation of a noisy signal is studied by deducing the theoretical expression of frequency estimation variance. Finally, the proposed IWPD is validated by extensive computer simulations and practical experiments. [ABSTRACT FROM AUTHOR]