Abstract: Random variation of sea waves is one of the typical characteristics of sea surface environment, and it will usually have an important influence on ocean communication system. The traditional parabolic equation model fails to fully consider the electromagnetic scattering and the shadow effect of the sea waves when the electromagnetic wave propagation over the rough sea surface. Aiming at this problem, by introducing the dynamic fractal method, an improved model based on the three-dimensional parabolic equation is proposed in this paper. The improved model is compared with the traditional Miller-Brown approximation method, and the results show that the former can better reflect the influence of the geometrical characteristics of the sea waves on the radio propagation.Furthermore, the effective detection range of the shipboard radar is simulated, and the radio propagation characteristics over the rough sea surface are analyzed, which shows that the proposed model is effective.