Under asynchronous sampling and non-integral period truncation conditions, there is a spectrum leakage problem and the occurrence of the picket fence effect in the harmonic analysis of power system with the fast Fourier transform (FFT) technique. Thus, accurate harmonic parameters can’t be achieved. Although the signal weighted by traditional windows can suppress the spectrum leakages, the analysis result is restricted by the sidelobe characteristics of these windows. An improved phase difference method based on variation semi-sinusoidal window for power harmonic analysis is proposed. A new window is applied to weight the signal in this method. Then, the improved phase difference method is employed to calculate the parameters of the signal, such as frequency, amplitude and phase．The satisfying performance of the sidelobe of variation semi-sinusoidal window can be obtained by adjusting the value of index. It can suppress errors caused by spectral leakage and implement flexible in practical engineering. Moreover, the calculation formulae of the frequencies, amplitudes and initial phases of fundamental and harmonics have been deduced．The simulation results indicate that the proposed method can estimate harmonic parameters with high accuracy.