Based on the Longuet-Higgins wave model theory, a modified phase modulation method of simulating freak waves is improved in this paper. The method can generate freak waves at assigned time and place, and their waveforms can not only maintain the frequency spectrum structure of the target spectrum and also satisfy the wave series statistics to a great extent. Then, the electromagnetic backscattering model of freak and background wave is established by the finite difference time domain method and the two-scale method. After averaging relative deviation and analyzing the error of the root mean square deviation within the measurement uncertainties, considering the computational efficiency, we use the two-scale model method to calculate the electromagnetic scattering coefficient of freak wave. Numerical results show that the normalized radar cross section (NRCS) of freak wave is much smaller than that of background wave. On the other hand, we analyze the electromagnetic scattering properties of freak waves under the different polarization modes, incident angles and incident frequencies. We find that in the condition of grazing incidence, the backscatter coefficient of freak wave increases with the increase of the incident frequency, but the increase amplitude is reduced, which meets the rough surface scattering theory. When the incident frequency is fixed and the incident〉is small, the backscatter coefficient calculation results of freak wave are similar under the condition of different polarizations VV's and HH's, but the backscatter coefficient of freak wave decreases obviously with the increase of incident angle, which is caused by the radar electromagnetic wave that is parallel to the sea surface and contacts it gradually. In addition, we find that the backscatter coefficient calculation result of freak waves under the VV polarization is much higher than under HH polarization from the two groups of experimental figures. According to the result of datum analysis, a conclusion is drawn that we can determine where the freak wave is when the NRCS difference of synthetic aperture radar (SAR) image is smaller than -11.8 dB. In the practical engineering application, the characteristic parameters are difficult to observe, while the difference in electromagnetic scattering coefficient between freak wave and background wave can be calculated from the SAR image of sea surface. This conclusion provides a reference standard for predicting the freak waves in engineering application, through which we can calculate the characteristic parameters of freak wave, determine its position, and study the electromagnetic scattering characteristics under the different polarization modes, incident angles and incident frequencies in future researches.