The Wen's wave spectrum model is adopted to describe the rough sea surface, and the relation between wind and ocean waves using sea wave spectrum theory is derived. The improved discrete mixed Fourier transform algorithm and the modified rader scattering coefficient model are used to calculate radio propagation loss and radar cross section respectively. On this basis, the influence of wind waves on radar echoes in the environment of atmosphere ducts is analysed by using numerical calculations. The results show that the influences of wind on propagation loss at different heights are different; wich respect to the propagation loss, rader scattering coefficient influenced by waves of factors is large, which results in large change in the radar echo power.