Abstract: Fast Fourier transform（FFT） is an effective analysis method for harmonics, and reduce the computational complexity to a great extent. FFT has the picket fence effect which leads to the observation error. The observation error from picket fence effect can be revised by the interpolated algorithm. However, the number of sampling data must satisfy certain conditions, which is not conducive to flexible set of sampling data. When the number of the sampling data is non radix-2, the paper calculated FFT through zero padding method to satisfy radix-2, and analyzed theoretically the interpolated FFT algorithm formula with the zero padding. The analysis results show that when the sampling data is non radix-2, the interpolated FFT algorithm and the interpolated discrete Fourier transform（DFT） algorithm are equivalent. It is more flexible in sampling data set, and does not need to satisfy the radix-2 conditions. Combining with the applications of 400 Hz AC power supply system, the paper validate the practicability and effectiveness of the algorithm through the simulation and experimental results.