In order to fast and accurately calculate the composite scattering from time-varying sea surfaces with a Low-flying small target above it, a hybrid algorithm of Kirchhoff approximation (KA) and method method-of-moments (MoM) is utilized in this paper for analyzing the Doppler spectrum signatures of Low-flying small target located above rough sea surfaces. The effect of sea state parameters, incidence angles, the speed of flying target, the distance between the target and the sea surfaces, the shape of the target’ cross-section on Doppler spectrum signatures of a low-flying small target above time-varying sea surface is investigated in detail in this paper.