The national standard GB/T 15543-2008 requires that the calculation of the voltage imbalance factor needs to obtain the phase sequence component based on the amplitude and phase of the fundamental wave, but its calculation method involves square root calculation and phase angle calculation, which is not conducive to the implementation of embedded systems. Therefore, a novel B-N mutual convolution window is established, the improved FFT correction formula which is based on the novel B-N mutual convolution window and the three-spectral line is derived, the phase sequence component is obtained by using the improved coordinate partition method, and three-phase imbalance factor detection based on novel B-N window and improved partition method is proposed in this paper. Complex square calculation is avoided and the detection accuracy of the amplitude and phase of the fundamental wave is improved, finally, the accurate detection of the three-phase imbalance factor is realized. The simulation experiment results show that the proposed algorithm can effectively achieve the accurate detection of imbalance factor under the conditions of fundamental wave, harmonic and noise interference, the implementation is simple and the accuracy is higher than the recommended method of the national standard.