There is difficult for Fast Fourier Transform to obtain the exact harmonic parameters in situation of non-synchronized sampling and non-interger cycle truncation. Utilization of window functions and interpolation algorithms can improve the accuracy of FFT. The spectral characteristics of Nuttall window are analyzed and an algorithm based on Nuttall window four-spectrum-line interpolation FFT is proposed to analyze electric power harmonic. The algorithm has improved the accuracy of harmonic analysis by using weighted arithmetic of four spectral lines near the peak spectrum-line frequency point. The applicable formulas are obtained by fitting of polynomials. Simulation results verify a higher accuracy of harmonic analysis and a better effect of restraining the spectral leakage in non-synchronized sampling by using the algorithm.