The improved phase modulation method is used to numerically simulate a two-dimensional freak wave. While generating freak waves at specific positions, the spectral structure of the target spectrum can also be maintained, and the statistical characteristics of wave sequences can be satisfied. The numerical simulation process is discussed in detail from the perspective of different wave spectra and other parameters, the priority applicability of the Joint North Sea Wave Project (JONSAWP) spectrum is determined, and the accuracy of the numerical simulation is significantly improved. At the same time, the electromagnetic scattering characteristics of freak waves are studied based on the two-scale method (TSM). The calculation results of normalized radar cross section (NRCS) under different wave spectra and different polarization modes are compared, and the effects of wind speed, incident frequency, and incident angle on the calculation results are discussed. Experiments show that the NRCS of the freak wave is obviously lower than the background wave, and the calculation of the NRCS is relatively simple. This provides an effective reference for radar detection of freak waves in offshore engineering. © 2022 by the authors.