The IEC standard 61000415 recommends that the sinusoidal and rectangular wave modulations are used to test flicker meter. At present, the researches on voltage flicker detection mainly focus on the sinusoidal wave modulation model, while there are few researches on the quick and accurate detection of the flicker under rectangular wave modulation that is more sensitive to human eyes. Aiming at the quick and accurate detection of the flicker under rectangular wave modulation, a fluctuation component extraction algorithm based on interval sampling improved energy operator is established and a new optimized KRV mutual convolution window function is built. An improved fast Fourier transformation (FFT) spectrum analysis method based on the threespectral line interpolation and new KRV deconvolution window is also derived. Based on this, the flicker detection method with rectangular wave modulation based on improved energy operator and new KRV mutual convolution window is proposed in this paper, and the voltage flicker parameter detection platform based on PXI + LabVIEW architecture is developed. The simulation and experiment results show that the proposed algorithm can effectively realize accurate detection and analysis of the flicker, and has higher accuracy compared with the traditional method in the cases of simple rectangular wave modulation, multifrequency modulation, containing all kinds of harmonic interferences, network fundamental frequency deviation and containing noise interference.